4MCH

Crystal structure of uridine phosphorylase from vibrio fischeri es114 complexed with 6-hydroxy-1-naphthoic acid, NYSGRC Target 029520.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LNHPDB ENTRY 4LNH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.2 M AMMONIUM SULFATE, 0.1 M HEPES:NAOH, PH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5351.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 163.975α = 90
b = 163.975β = 90
c = 58.355γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2013-08-13SAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9791APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.7319.75399.60.1030.1037.97.231147
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.821000.0151.5020.57.14558

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4LNH1.7319.1631134157099.560.17410.17290.1962RANDOM34.5311
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]
-9.21-9.2118.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.096
r_dihedral_angle_4_deg20.072
r_dihedral_angle_3_deg11.902
r_dihedral_angle_1_deg5.942
r_scbond_it2.49
r_mcangle_it2.466
r_mcbond_it1.537
r_angle_refined_deg1.196
r_chiral_restr0.083
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.096
r_dihedral_angle_4_deg20.072
r_dihedral_angle_3_deg11.902
r_dihedral_angle_1_deg5.942
r_scbond_it2.49
r_mcangle_it2.466
r_mcbond_it1.537
r_angle_refined_deg1.196
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1886
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms75

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction