4Z3K | pdb_00004z3k

Human sepiapterin reductase in complex with the cofactor NADP+ and the trypthophan metabolite xanthurenic acid

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	2% W/V PEG1000, 1.9 M Ammonium sulfate, 0.1 M Hepes pH7.5

Crystal Properties
Matthews coefficient	Solvent content
4.89	74.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.964	α = 90
b = 143.964	β = 90
c = 180.74	γ = 120

Symmetry
Space Group	P 61

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 2M-F		2014-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	2.35	124.676	100	0.106	0.111	0.031	20	12.9	88165	88165			57.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.48	100		1.085	1.085	0.307	0.7	13.3	12862

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4HWK	2.35	124.676	83471	4633	99.99	0.1825	0.1808	0.19	0.2139	RANDOM	50.093

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]
0.83	0.41		0.83		-2.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.316
r_dihedral_angle_4_deg	20.15
r_dihedral_angle_3_deg	13.857
r_dihedral_angle_1_deg	6.388
r_mcangle_it	6.24
r_mcbond_it	4.453
r_mcbond_other	4.451
r_angle_refined_deg	1.446
r_angle_other_deg	0.732
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.316
r_dihedral_angle_4_deg	20.15
r_dihedral_angle_3_deg	13.857
r_dihedral_angle_1_deg	6.388
r_mcangle_it	6.24
r_mcbond_it	4.453
r_mcbond_other	4.451
r_angle_refined_deg	1.446
r_angle_other_deg	0.732
r_chiral_restr	0.085
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7744
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	286

Software

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

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.