9QL0 | pdb_00009ql0

E. coli IspH crystallized in the presence of adenosine hemisulfate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MUY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	27.5% (w/v) PEG 3350, 150 mM (NH4)2SO4, 100 mM Bis-Tris pH 6.5, 5 mM adenosine hemisulfate

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.909	α = 90
b = 81.291	β = 90
c = 112.871	γ = 90

Symmetry
Space Group	P 21 21 21

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 X 16M		2024-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033420	PETRA III, DESY	P11

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	1.85	47.361	99.4	0.292	0.315	0.117	0.996	7.9	13.5		53566

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	1.85	1.89	99.1		2.517	2.713	1.008	0.63	1.4	13.6

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	NONE	1.852	47.361	53500	2784	99.225	0.211	0.2084	0.2039	0.2533	0.2497	26.429

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]
-1.108			-1.252		2.359

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.599
r_dihedral_angle_6_deg	14.732
r_dihedral_angle_2_deg	8.813
r_lrange_other	6.985
r_lrange_it	6.984
r_dihedral_angle_1_deg	6.149
r_scangle_other	5.846
r_scangle_it	5.844
r_scbond_it	3.714
r_scbond_other	3.71
r_mcangle_it	3.154
r_mcangle_other	3.153
r_mcbond_it	2.18
r_mcbond_other	2.178
r_angle_refined_deg	1.837
r_angle_other_deg	0.628
r_nbd_other	0.256
r_nbd_refined	0.219
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.195
r_xyhbond_nbd_refined	0.191
r_symmetry_nbd_refined	0.187
r_nbtor_refined	0.172
r_metal_ion_refined	0.133
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4920
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling
MOLREP	phasing