3ZPI

PikC D50N mutant in P21 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZK5PDB ENTRY 3ZK5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.512% PEG3350, 5% TACSIMATE 5.5, 0.1 M NA/K TARTRATE
Crystal Properties
Matthews coefficientSolvent content
2.2445.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.085α = 90
b = 59.784β = 95.81
c = 91.267γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMIRRORS2013-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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
11.6390.899.10.069.53.81008741.522.6
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)
11.631.7294.10.561.63

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 3ZK51.6390.895780503798.950.176110.17390.21874RANDOM22.735
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]
0.19-0.580.23-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.532
r_dihedral_angle_4_deg20.016
r_dihedral_angle_3_deg13.22
r_dihedral_angle_1_deg5.815
r_scangle_it5.333
r_scbond_it3.437
r_mcangle_it2.23
r_angle_refined_deg2.138
r_mcbond_it1.386
r_chiral_restr0.157
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.532
r_dihedral_angle_4_deg20.016
r_dihedral_angle_3_deg13.22
r_dihedral_angle_1_deg5.815
r_scangle_it5.333
r_scbond_it3.437
r_mcangle_it2.23
r_angle_refined_deg2.138
r_mcbond_it1.386
r_chiral_restr0.157
r_bond_refined_d0.026
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_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6124
Nucleic Acid Atoms
Solvent Atoms880
Heterogen Atoms153

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing