1Z82

Crystal structure of glycerol-3-phosphate dehydrogenase (TM0378) from THERMOTOGA MARITIMA at 2.00 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP82770.2M MgCl2, 35.0% MPD, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0339.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.09α = 90
b = 67.451β = 113.67
c = 75.597γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-02-27MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.891940,0.979245SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1229.8198.40.0837.23.540008
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0598.50.5581.33.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT229.8137984202498.340.1680.168240.1660.211RANDOM29.469
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]
3.370.87-0.29-2.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.88
r_dihedral_angle_4_deg20.557
r_dihedral_angle_3_deg15.171
r_dihedral_angle_1_deg5.536
r_scangle_it3.441
r_scbond_it2.346
r_angle_refined_deg1.621
r_mcangle_it1.284
r_mcbond_it1.052
r_angle_other_deg1.032
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.88
r_dihedral_angle_4_deg20.557
r_dihedral_angle_3_deg15.171
r_dihedral_angle_1_deg5.536
r_scangle_it3.441
r_scbond_it2.346
r_angle_refined_deg1.621
r_mcangle_it1.284
r_mcbond_it1.052
r_angle_other_deg1.032
r_symmetry_vdw_other0.233
r_nbd_refined0.212
r_mcbond_other0.209
r_nbd_other0.182
r_nbtor_refined0.18
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.157
r_chiral_restr0.085
r_nbtor_other0.085
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4812
Nucleic Acid Atoms
Solvent Atoms323
Heterogen Atoms180

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing