6C56 | pdb_00006c56

Crystal structure of mutant human geranylgeranyl pyrophosphate synthase (Y246D) in its Apo form

X-RAY DIFFRACTION

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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, SITTING DROP		295	0.26 M ammonium phosphate, 35% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.1	α = 90
b = 185.1	β = 90
c = 115.2	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX-300		2016-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.8	54.39	99.9	0.039	0.014	36.5	9.9		24791

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.88	99.7		1.129	0.397	2.2	10

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2Q80	2.8	54.39	23520	1270	99.89	0.18804	0.18522	0.19	0.2381	0.24	RANDOM	100.055

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]
-1.88			-1.88		3.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.929
r_dihedral_angle_4_deg	17.993
r_dihedral_angle_3_deg	17.882
r_long_range_B_refined	7.726
r_long_range_B_other	7.725
r_dihedral_angle_1_deg	7.042
r_scangle_other	6.025
r_mcangle_it	4.903
r_mcangle_other	4.902
r_scbond_it	4.089
r_scbond_other	4.088
r_mcbond_it	3.353
r_mcbond_other	3.351
r_angle_refined_deg	2.167
r_angle_other_deg	1.205
r_chiral_restr	0.112
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4316
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	25

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing