1YWP

Phospholipase Cgamma1 SH3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9298PEG 4000, sodium acetate, Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
1.831.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.967α = 90
b = 31.28β = 97.09
c = 29.778γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152004-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.009NSLSX29A

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
11.65097.50.03742.2697914
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)
1.61.6694.50.16810.5

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 1OEB1.629.49660432397.450.144570.14240.18774RANDOM17.417
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]
2.110.67-1.01-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.599
r_dihedral_angle_3_deg10.804
r_dihedral_angle_4_deg7.993
r_dihedral_angle_1_deg6.864
r_scangle_it4.52
r_scbond_it3.116
r_mcangle_it1.91
r_angle_refined_deg1.677
r_mcbond_it1.28
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.599
r_dihedral_angle_3_deg10.804
r_dihedral_angle_4_deg7.993
r_dihedral_angle_1_deg6.864
r_scangle_it4.52
r_scbond_it3.116
r_mcangle_it1.91
r_angle_refined_deg1.677
r_mcbond_it1.28
r_nbtor_refined0.32
r_nbd_refined0.214
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.177
r_symmetry_vdw_refined0.172
r_chiral_restr0.137
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms512
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing