3BGG

Crystal structure of Human Orotidine 5'-monophosphate Decarboxylase complexed with BMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P1F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.4293Ammonium Sulfate, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.596α = 90
b = 116.886β = 90
c = 61.985γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90020APS14-BM-C

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
11.935095.30.130.137.572130620304
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)
1.931.9674.60.50.52.185.6818

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2P1F1.93502130619516104895.150.182740.181260.21068RANDOM27.081
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]
5.44-2.37-3.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.096
r_dihedral_angle_4_deg17.653
r_dihedral_angle_3_deg12.678
r_dihedral_angle_1_deg6.345
r_scangle_it4.14
r_scbond_it2.587
r_angle_refined_deg1.546
r_mcangle_it1.451
r_mcbond_it1.034
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.096
r_dihedral_angle_4_deg17.653
r_dihedral_angle_3_deg12.678
r_dihedral_angle_1_deg6.345
r_scangle_it4.14
r_scbond_it2.587
r_angle_refined_deg1.546
r_mcangle_it1.451
r_mcbond_it1.034
r_nbtor_refined0.306
r_nbd_refined0.205
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.139
r_chiral_restr0.108
r_symmetry_hbond_refined0.082
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2025
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building