5DOT

Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JDB1JDB, 2YVQ
experimental modelPDB 2YVQ1JDB, 2YVQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.229420% PEG3350, 0.2 M tri-sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.8256.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.337α = 90
b = 133.482β = 102.51
c = 142.907γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.96112ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.4139.51696.30.1140.1350.0717.93.513659513659528.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5383.40.3420.3420.21223.517237

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 REPLACEMENTTHROUGHOUT1JDB, 2YVQ2.443.95136557684996.130.16620.16460.1964RANDOM40.365
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]
-0.21-0.271.19-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.133
r_dihedral_angle_4_deg15.823
r_dihedral_angle_3_deg13.463
r_dihedral_angle_1_deg5.708
r_mcangle_it4.557
r_mcbond_it2.929
r_mcbond_other2.929
r_angle_refined_deg1.293
r_angle_other_deg0.835
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.133
r_dihedral_angle_4_deg15.823
r_dihedral_angle_3_deg13.463
r_dihedral_angle_1_deg5.708
r_mcangle_it4.557
r_mcbond_it2.929
r_mcbond_other2.929
r_angle_refined_deg1.293
r_angle_other_deg0.835
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20944
Nucleic Acid Atoms
Solvent Atoms819
Heterogen Atoms46

Software

Software
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction