2GCG | pdb_00002gcg

Ternary Crystal Structure of Human Glyoxylate Reductase/Hydroxypyruvate Reductase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GDH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	291	15% PEG 8000, 0.2M ammonium sulfate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.7	53.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.568	α = 90
b = 66.877	β = 98.22
c = 149.78	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	ADSC QUANTUM 4		2005-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1	1.488	SRS	PX14.1

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	2.2	50	90.3	0.121	7.5	2.6		69070

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	2.2	2.28	72.3	72.3	0.275		2.2

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-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	THROUGHOUT	1GDH	2.2	46.2	69056	3460	90.02	0.205	0.205	0.201	0.21	0.282	0.29	RANDOM	33.362

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]
-0.09		-1.68	-1.72		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.513
r_dihedral_angle_4_deg	20.106
r_dihedral_angle_3_deg	19.406
r_dihedral_angle_1_deg	6.888
r_scangle_it	2.932
r_scbond_it	2.035
r_angle_refined_deg	1.857
r_mcangle_it	1.128
r_mcbond_it	0.706
r_nbtor_refined	0.305
r_nbd_refined	0.225
r_symmetry_hbond_refined	0.184
r_xyhbond_nbd_refined	0.178
r_symmetry_vdw_refined	0.174
r_chiral_restr	0.127
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9859
Nucleic Acid Atoms
Solvent Atoms	611
Heterogen Atoms	231

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing