1O4V

Crystal structure of the catalytic subunit of a phosphoribosylaminoimidazole mutase (tm0446) from thermotoga maritima at 1.77 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QCZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP5.62932M ammonium sulfate, 0.1M tri-sodium citrate dihydrate pH 5.6, 0.2M potassium sodium tartrate tetrahydrate , VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.249α = 90
b = 103.249β = 90
c = 65.445γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315flat mirror2003-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-1SSRLBL11-1

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
11.7724.3795.40.07219.37.2166971669734.3
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)
11.771.8273.80.4522.13.5931

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1QCZ1.7724.371585983895.170.15140.149810.18177RANDOM26.807
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]
-2.05-2.054.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.012
r_dihedral_angle_3_deg14.792
r_dihedral_angle_4_deg14.694
r_dihedral_angle_1_deg5.245
r_scangle_it4.544
r_scbond_it2.684
r_mcangle_it1.589
r_angle_refined_deg1.468
r_angle_other_deg0.927
r_mcbond_it0.873
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.012
r_dihedral_angle_3_deg14.792
r_dihedral_angle_4_deg14.694
r_dihedral_angle_1_deg5.245
r_scangle_it4.544
r_scbond_it2.684
r_mcangle_it1.589
r_angle_refined_deg1.468
r_angle_other_deg0.927
r_mcbond_it0.873
r_symmetry_vdw_refined0.314
r_symmetry_hbond_refined0.243
r_nbd_refined0.223
r_xyhbond_nbd_refined0.21
r_symmetry_vdw_other0.209
r_nbd_other0.176
r_chiral_restr0.093
r_nbtor_other0.085
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1280
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms10

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling