8XSV

crystal structure of PPAT mutant P8A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OTW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Lithium sulfate, PEG500 MME
Crystal Properties
Matthews coefficientSolvent content
2.6152.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.893α = 90
b = 126.898β = 90
c = 89.98γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
1289.9897.90.9621.62.375207
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.050.75

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 REPLACEMENTTHROUGHOUT3OTW289.9868551366195.960.198420.195690.25016RANDOM29.379
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]
0.12-0.08-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.656
r_dihedral_angle_4_deg19.672
r_dihedral_angle_3_deg18.841
r_sphericity_free17.622
r_rigid_bond_restr16.174
r_sphericity_bonded10.517
r_dihedral_angle_1_deg6.732
r_angle_refined_deg2.485
r_chiral_restr0.186
r_bond_refined_d0.027
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.656
r_dihedral_angle_4_deg19.672
r_dihedral_angle_3_deg18.841
r_sphericity_free17.622
r_rigid_bond_restr16.174
r_sphericity_bonded10.517
r_dihedral_angle_1_deg6.732
r_angle_refined_deg2.485
r_chiral_restr0.186
r_bond_refined_d0.027
r_gen_planes_refined0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7350
Nucleic Acid Atoms
Solvent Atoms619
Heterogen Atoms264

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing