4XWY | pdb_00004xwy

Crystal structure of human sepiapterin reductase in complex with an N-acetylserotinin analogue

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, 2.5% V/V glycerol, 1.7 M Ammonium sulfate, 0.1 M Hepes

Crystal Properties
Matthews coefficient	Solvent content
4.58	73.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.84	α = 90
b = 144.84	β = 90
c = 180.695	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 6M		2014-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.99999	SLS	X06SA

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	125.435	100	0.096	0.1	0.03	15.8	11.2	89220	89220			55.8

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		0.716	0.716	0.22	1	11.5	13018

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	MOLECULAR REPLACEMENT	FREE R-VALUE	4HWK	2.35	125.435	84419	4682	99.91	0.1868	0.1852	0.19	0.2167	0.19	RANDOM	48.374

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]
0.67	0.33		0.67		-2.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.2
r_dihedral_angle_4_deg	22.307
r_dihedral_angle_3_deg	15.712
r_mcangle_it	6.449
r_dihedral_angle_1_deg	6.414
r_mcbond_it	4.664
r_mcbond_other	4.662
r_angle_refined_deg	1.219
r_angle_other_deg	0.658
r_chiral_restr	0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.2
r_dihedral_angle_4_deg	22.307
r_dihedral_angle_3_deg	15.712
r_mcangle_it	6.449
r_dihedral_angle_1_deg	6.414
r_mcbond_it	4.664
r_mcbond_other	4.662
r_angle_refined_deg	1.219
r_angle_other_deg	0.658
r_chiral_restr	0.065
r_gen_planes_refined	0.012
r_bond_refined_d	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7744
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	313

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
REFMAC	refinement
Coot	model building
MOLREP	phasing
SCALA	data scaling
XDS	data reduction

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.