1VJO

Crystal structure of Alanine--glyoxylate aminotransferase (ALR1004) from Nostoc sp. at 1.70 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP2930.06M HEPES, 0.04M HEPES_Na, 12% PEG MME 5000, 0.2M NP_Calcium Chloride , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0639.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.258α = 90
b = 101.057β = 90
c = 97.252γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHbent conical Si-mirror (Rh coating)2003-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C

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
11.731.1899.20.09311.85.44275926.42
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)
11.71.741000.722253161

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.731.1837725204391.970.153830.151350.20182RANDOM23.148
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]
0.07-0.01-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.776
r_dihedral_angle_4_deg16.602
r_dihedral_angle_3_deg13.278
r_dihedral_angle_1_deg5.726
r_scangle_it3.76
r_scbond_it2.606
r_angle_refined_deg1.591
r_mcangle_it1.294
r_mcbond_it1.077
r_symmetry_hbond_refined0.251
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.776
r_dihedral_angle_4_deg16.602
r_dihedral_angle_3_deg13.278
r_dihedral_angle_1_deg5.726
r_scangle_it3.76
r_scbond_it2.606
r_angle_refined_deg1.591
r_mcangle_it1.294
r_mcbond_it1.077
r_symmetry_hbond_refined0.251
r_symmetry_vdw_refined0.206
r_nbd_refined0.201
r_xyhbond_nbd_refined0.184
r_chiral_restr0.113
r_bond_refined_d0.018
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2904
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms16

Software

Software
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
SHELXDphasing
REFMACrefinement
CCP4data scaling