5QIF | pdb_00005qif

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z31792168

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.75	293	0.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.78	α = 90
b = 97.78	β = 90
c = 81.268	γ = 90

Symmetry
Space Group	I 4

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 PILATUS 6M		2018-01-27		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

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	1.2	26.33	82.2	0.035	0.039	0.015	0.999	25	4.7		97888

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	1.2	1.23	15.7		0.357	0.505	0.357	0.787		1.1	1369

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	FOURIER SYNTHESIS	THROUGHOUT	2NZL	1.2	69.14	92992	4888	82.2	0.1641	0.163	0.17	0.1829	0.19	RANDOM	14.218

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]
-0.4			-0.4		0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.111
r_dihedral_angle_4_deg	14.641
r_dihedral_angle_3_deg	11.798
r_sphericity_free	10.509
r_dihedral_angle_1_deg	6.181
r_sphericity_bonded	3.987
r_rigid_bond_restr	2.078
r_angle_refined_deg	1.639
r_mcangle_it	1.314
r_mcbond_it	1.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.111
r_dihedral_angle_4_deg	14.641
r_dihedral_angle_3_deg	11.798
r_sphericity_free	10.509
r_dihedral_angle_1_deg	6.181
r_sphericity_bonded	3.987
r_rigid_bond_restr	2.078
r_angle_refined_deg	1.639
r_mcangle_it	1.314
r_mcbond_it	1.086
r_mcbond_other	1.082
r_angle_other_deg	1.033
r_chiral_restr	0.103
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2723
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

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.