5QIG | pdb_00005qig

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z1407672867

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
2.35	47.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.54	α = 90
b = 97.54	β = 90
c = 80.646	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		2018-01-29		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	1.42	26.21	99.8	0.045	0.049	0.019	0.999	19.1	5.7		71180

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	1.42	1.46	98.5		0.551	0.65	0.34	0.754		3.5	5192

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	1.42	68.97	67577	3597	99.84	0.157	0.1554	0.16	0.1868	0.19	RANDOM	19.117

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]
-0.66			-0.66		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.259
r_dihedral_angle_4_deg	13.928
r_sphericity_free	13.621
r_dihedral_angle_3_deg	12.377
r_sphericity_bonded	7.5
r_dihedral_angle_1_deg	6.163
r_mcangle_it	2.512
r_rigid_bond_restr	2.286
r_mcbond_it	2.014
r_mcbond_other	1.997

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.259
r_dihedral_angle_4_deg	13.928
r_sphericity_free	13.621
r_dihedral_angle_3_deg	12.377
r_sphericity_bonded	7.5
r_dihedral_angle_1_deg	6.163
r_mcangle_it	2.512
r_rigid_bond_restr	2.286
r_mcbond_it	2.014
r_mcbond_other	1.997
r_angle_refined_deg	1.65
r_angle_other_deg	1.042
r_chiral_restr	0.11
r_bond_refined_d	0.014
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	2715
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	75

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.