9ZB8 | pdb_00009zb8

Crystal Structure of Human GGPPS Bound to Selective Inhibitor CML-07-119

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q80

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293.15	100 mM Tris-HCl pH 8.0, 42% 2-Methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.413	α = 90
b = 116.167	β = 99.272
c = 214.406	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M	Microfocus	2024-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-1	0.97946	SSRL	BL12-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.64	106.03	45.6	0.167	0.18	0.067	0.996	4.3	6.9		54508			32.88

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.64	3.26	9.1		0.483	0.524	0.202	0.809	1.6	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.641	106.027	54505	2757	45.448	0.211	0.2088	0.2088	0.2473	0.248	54.025

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.601		1.08	-2.576		1.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.702
r_dihedral_angle_6_deg	14.108
r_dihedral_angle_2_deg	10.791
r_lrange_it	5.525
r_lrange_other	5.525
r_dihedral_angle_1_deg	5.503
r_scangle_it	3.346
r_scangle_other	3.346
r_mcangle_it	2.794
r_mcangle_other	2.794

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.702
r_dihedral_angle_6_deg	14.108
r_dihedral_angle_2_deg	10.791
r_lrange_it	5.525
r_lrange_other	5.525
r_dihedral_angle_1_deg	5.503
r_scangle_it	3.346
r_scangle_other	3.346
r_mcangle_it	2.794
r_mcangle_other	2.794
r_scbond_it	1.946
r_scbond_other	1.946
r_mcbond_it	1.614
r_mcbond_other	1.614
r_angle_refined_deg	1.61
r_angle_other_deg	0.522
r_symmetry_nbd_refined	0.386
r_nbd_other	0.274
r_nbd_refined	0.243
r_xyhbond_nbd_refined	0.22
r_nbtor_refined	0.197
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_other	0.152
r_metal_ion_refined	0.119
r_ncsr_local_group_30	0.091
r_ncsr_local_group_21	0.09
r_ncsr_local_group_38	0.085
r_ncsr_local_group_60	0.085
r_ncsr_local_group_45	0.084
r_ncsr_local_group_65	0.084
r_ncsr_local_group_63	0.083
r_ncsr_local_group_11	0.082
r_ncsr_local_group_56	0.082
r_ncsr_local_group_66	0.082
r_symmetry_nbtor_other	0.077
r_ncsr_local_group_12	0.077
r_ncsr_local_group_51	0.075
r_ncsr_local_group_24	0.074
r_ncsr_local_group_22	0.073
r_ncsr_local_group_23	0.073
r_ncsr_local_group_28	0.072
r_ncsr_local_group_26	0.071
r_ncsr_local_group_29	0.07
r_ncsr_local_group_2	0.068
r_ncsr_local_group_25	0.068
r_ncsr_local_group_27	0.068
r_chiral_restr	0.067
r_ncsr_local_group_15	0.066
r_ncsr_local_group_18	0.066
r_ncsr_local_group_1	0.065
r_ncsr_local_group_7	0.065
r_ncsr_local_group_19	0.064
r_ncsr_local_group_5	0.062
r_ncsr_local_group_13	0.062
r_ncsr_local_group_16	0.062
r_ncsr_local_group_17	0.062
r_ncsr_local_group_14	0.061
r_ncsr_local_group_33	0.061
r_ncsr_local_group_47	0.061
r_ncsr_local_group_49	0.06
r_ncsr_local_group_32	0.059
r_ncsr_local_group_42	0.059
r_ncsr_local_group_43	0.059
r_ncsr_local_group_46	0.059
r_ncsr_local_group_52	0.059
r_ncsr_local_group_3	0.058
r_ncsr_local_group_35	0.058
r_ncsr_local_group_54	0.058
r_ncsr_local_group_6	0.057
r_ncsr_local_group_20	0.057
r_ncsr_local_group_34	0.057
r_ncsr_local_group_39	0.057
r_ncsr_local_group_40	0.057
r_ncsr_local_group_41	0.057
r_ncsr_local_group_62	0.057
r_ncsr_local_group_4	0.056
r_ncsr_local_group_9	0.056
r_ncsr_local_group_57	0.056
r_ncsr_local_group_53	0.055
r_ncsr_local_group_58	0.055
r_ncsr_local_group_61	0.055
r_ncsr_local_group_10	0.054
r_ncsr_local_group_31	0.054
r_ncsr_local_group_48	0.054
r_ncsr_local_group_8	0.053
r_ncsr_local_group_64	0.052
r_ncsr_local_group_50	0.051
r_ncsr_local_group_55	0.051
r_ncsr_local_group_59	0.05
r_ncsr_local_group_37	0.049
r_ncsr_local_group_36	0.046
r_ncsr_local_group_44	0.045
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28451
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	480

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
STARANISO	data scaling
PHASER	phasing

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.