4R00

yCP beta5-C52F mutant in complex with Omuralide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 MM MGAC2, 13% MPD, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.25α = 90
b = 301.24β = 113.16
c = 144.33γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
12.83097.50.08711.126189825535122
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)
12.82.9970.5052.3

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1RYP2.8152553512425831276897.590.1880.18520.183890.20992RANDOM59.818
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]
2.54-0.7-4.61.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.63
r_sphericity_free26.022
r_sphericity_bonded16.45
r_dihedral_angle_3_deg13.58
r_dihedral_angle_4_deg12.486
r_dihedral_angle_1_deg4.918
r_long_range_B_refined3.828
r_long_range_B_other3.823
r_mcangle_it3.302
r_mcangle_other3.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.63
r_sphericity_free26.022
r_sphericity_bonded16.45
r_dihedral_angle_3_deg13.58
r_dihedral_angle_4_deg12.486
r_dihedral_angle_1_deg4.918
r_long_range_B_refined3.828
r_long_range_B_other3.823
r_mcangle_it3.302
r_mcangle_other3.302
r_scangle_other3.078
r_mcbond_it2.447
r_mcbond_other2.447
r_scbond_it2.422
r_scbond_other2.422
r_rigid_bond_restr1.204
r_angle_refined_deg0.846
r_angle_other_deg0.793
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49376
Nucleic Acid Atoms
Solvent Atoms343
Heterogen Atoms103

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing