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Crystal structure of the RhoGEF domain of human neuroepithelial cell-transforming gene 1 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z0Q pdb entry 2Z0Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 1.0M sodium citrate, 0.1M sodium cacodylate, 5% ethylene glycol,
crystallized in the presence of 1:100 (w/w) subtilisin, pH 4.8, vapor diffusion, hanging drop
Crystal Properties Matthews coefficient Solvent content 3.07 59.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.629 α = 90 b = 95.629 β = 90 c = 62.887 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2008-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97945 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.6 50 95.1 0.095 12.9 8.8 9673
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 65.3 0.526 2.3 645
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2Z0Q 2.6 30 9653 465 94.898 0.215 0.213 0.242 0.25 0.2569 RANDOM 33.152
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] -1.752 -0.876 -1.752 2.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.023 r_dihedral_angle_4_deg 23.591 r_dihedral_angle_3_deg 15.378 r_dihedral_angle_1_deg 4.982 r_scangle_it 1.845 r_mcangle_it 1.578 r_angle_refined_deg 1.123 r_scbond_it 1.063 r_mcbond_it 0.885 r_angle_other_deg 0.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.023 r_dihedral_angle_4_deg 23.591 r_dihedral_angle_3_deg 15.378 r_dihedral_angle_1_deg 4.982 r_scangle_it 1.845 r_mcangle_it 1.578 r_angle_refined_deg 1.123 r_scbond_it 1.063 r_mcbond_it 0.885 r_angle_other_deg 0.863 r_mcbond_other 0.129 r_chiral_restr 0.059 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1468 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling