5QIE

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with Z2856434894

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	47.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.677	α = 90
b = 97.677	β = 90
c = 80.414	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		2018-01-28		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	1.34	26.2	94.8	0.05	0.055	0.022	0.999	19.4	5.4		80351

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	1.34	1.37	61.8		0.638	0.791	0.455	0.802		2.7	3842

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2NZL	1.34	69.07	76297	4052	94.75	0.1663	0.1648	0.1927	RANDOM	17.532

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]
-0.72			-0.72		1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.105
r_dihedral_angle_4_deg	14.223
r_sphericity_free	12.285
r_dihedral_angle_3_deg	12.163
r_dihedral_angle_1_deg	6.308
r_sphericity_bonded	5.961
r_rigid_bond_restr	3.201
r_mcangle_it	2.073
r_angle_refined_deg	1.875
r_mcbond_other	1.725

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.105
r_dihedral_angle_4_deg	14.223
r_sphericity_free	12.285
r_dihedral_angle_3_deg	12.163
r_dihedral_angle_1_deg	6.308
r_sphericity_bonded	5.961
r_rigid_bond_restr	3.201
r_mcangle_it	2.073
r_angle_refined_deg	1.875
r_mcbond_other	1.725
r_mcbond_it	1.724
r_angle_other_deg	1.081
r_chiral_restr	0.125
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2669
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	59

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 National Science Foundation (DBI-1832184), 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 R01GM133198.