2PLA

Crystal structure of human glycerol-3-phosphate dehydrogenase 1-like protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1X0V	PDB entry 1X0V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	277	50% PEG 300, 0.2M Sodium chloride, 0.1M Sodium potassium phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4	69.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.1	α = 90
b = 139.1	β = 90
c = 109.62	γ = 120

Symmetry
Space Group	P 31 2 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		2007-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.79887	SLS	X10SA

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	2.51	50	99.7	0.061	19	7.5	42245	42245			67.6

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	2.51	2.66	98.5		0.621	3.39	7.5	6634

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 (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	PDB entry 1X0V	2.51	29.361	42226	42226	2127	99.63	0.177	0.177	0.175	0.18	0.212	0.2	RANDOM	28.714

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]
1.05	0.53		1.05		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.782
r_dihedral_angle_4_deg	19.987
r_dihedral_angle_3_deg	15.527
r_dihedral_angle_1_deg	5.338
r_scangle_it	1.924
r_angle_refined_deg	1.306
r_scbond_it	1.183
r_angle_other_deg	0.915
r_mcangle_it	0.708
r_mcbond_it	0.412
r_symmetry_vdw_other	0.255
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.191
r_nbd_other	0.178
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.143
r_symmetry_vdw_refined	0.112
r_nbtor_other	0.084
r_mcbond_other	0.072
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5155
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	104

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XDS	data scaling