2H1S

Crystal Structure of a Glyoxylate/Hydroxypyruvate reductase from Homo sapiens

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GDH	1GDH, 1WWK as a basis of 2-member ensemble
experimental model	PDB	1WWK	1GDH, 1WWK as a basis of 2-member ensemble

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.0003 M TCEP, 0.005 MES PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (12% PEG 3350, 0.10 M MOPS PH 7). Crystal was cryo-protected with 15% PEG 3350, 0.10 M PIPES PH 6.5 and a final concentration of 25% Ethylene glycol, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.996	α = 90
b = 66.436	β = 98.59
c = 148.774	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2006-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97928	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.45	49.326	93.3	0.157	7.087	6.2		50144

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.51	80.3		0.504	2.261	4.8	2832

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1GDH, 1WWK as a basis of 2-member ensemble	2.45	49.326	50129	2551	93.114	0.21	0.2072	0.2643	RANDOM	8.853

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]
-0.69		-1.165	-0.427		0.769

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.26
r_dihedral_angle_4_deg	22.585
r_dihedral_angle_3_deg	17.416
r_dihedral_angle_1_deg	6.344
r_scangle_it	5.649
r_scbond_it	3.723
r_mcangle_it	1.682
r_angle_refined_deg	1.59
r_mcbond_it	0.951
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.255
r_symmetry_vdw_refined	0.248
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.179
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9768
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction