2G76

Crystal structure of human 3-phosphoglycerate dehydrogenase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1 M MMT, 30 % PEG1k, 5mM NAD+, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.084	α = 90
b = 124.113	β = 100.99
c = 59.502	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 225 mm CCD		2006-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99806	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	36.2	98.9			66626	66626

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	96.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1YGY, 1PSD	1.7	36.2	63219	63219	3371	98.6	0.1828	0.18098	0.21644	RANDOM	25.461

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]
0.12		-0.08	2		-2.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.94
r_dihedral_angle_3_deg	12.983
r_dihedral_angle_4_deg	12.396
r_dihedral_angle_1_deg	5.893
r_scangle_it	2.637
r_scbond_it	1.759
r_angle_refined_deg	1.453
r_mcangle_it	1.014
r_angle_other_deg	0.932
r_mcbond_it	0.709
r_nbd_refined	0.221
r_nbd_other	0.199
r_symmetry_vdw_other	0.194
r_mcbond_other	0.186
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.139
r_symmetry_hbond_refined	0.129
r_nbtor_other	0.085
r_chiral_restr	0.081
r_symmetry_vdw_refined	0.046
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4413
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	106

Software

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