1VKZ

Crystal structure of Phosphoribosylamine--glycine ligase (TM1250) from Thermotoga maritima at 2.30 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP6.527718% PEG-8000, 0.1M sodium cacodylate pH 6.5, 0.2M calcium acetate hydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2VAPOR DIFFUSION,SITTING DROP,NANODROP727720% PEG-6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2946.21
2.4449.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.745α = 90
b = 78.443β = 95.06
c = 85.018γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2004-03-03MSINGLE WAVELENGTH
21x-ray100CCDAPSwater cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror2004-02-20MMAD
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1
2SYNCHROTRONAPS BEAMLINE 19-BM0.979127,0.979292,0.964063APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1,22.337.485.60.05412.123174954.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,22.32.3688.20.6321.31.92434

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 DIFFRACTIONMADTHROUGHOUT2.337.2629714156084.010.215720.213150.26383RANDOM44.622
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]
0.3-0.692.77-3.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.517
r_dihedral_angle_4_deg19.757
r_dihedral_angle_3_deg17.106
r_dihedral_angle_1_deg7.293
r_scangle_it7.017
r_scbond_it5.184
r_mcangle_it2.76
r_mcbond_it1.937
r_angle_refined_deg1.491
r_angle_other_deg0.811
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.517
r_dihedral_angle_4_deg19.757
r_dihedral_angle_3_deg17.106
r_dihedral_angle_1_deg7.293
r_scangle_it7.017
r_scbond_it5.184
r_mcangle_it2.76
r_mcbond_it1.937
r_angle_refined_deg1.491
r_angle_other_deg0.811
r_mcbond_other0.479
r_symmetry_vdw_other0.22
r_nbd_refined0.207
r_nbd_other0.183
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.177
r_symmetry_hbond_refined0.143
r_nbtor_other0.089
r_chiral_restr0.083
r_xyhbond_nbd_other0.057
r_bond_refined_d0.016
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6065
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms4

Software

Software
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
REFMACrefinement
CCP4data scaling