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Structure of human MDM2 protein in complex with a small molecule inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 300 0.1M sodium-acetate-trihydrate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 1.97 37.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.46 α = 90 b = 60.46 β = 90 c = 48.05 γ = 90
Symmetry Space Group P 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD MAR CCD 165 mm monochromator, mirror 2009-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 SLS X10SA
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 2.2 30 88.6 0.079 12.1 7896 6949 2 2
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) 2.2 2.3 80.4 0.502 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1RV1 2.3 20 2 6949 6613 323 88.61 0.21 0.20942 0.20745 0.21 0.25145 0.2572 RANDOM 39.097
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] 1.28 1.28 -2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.586 r_dihedral_angle_4_deg 28.761 r_dihedral_angle_3_deg 20.756 r_dihedral_angle_1_deg 7.597 r_scangle_it 3.169 r_scbond_it 1.896 r_angle_refined_deg 1.695 r_mcangle_it 1.59 r_angle_other_deg 0.948 r_mcbond_it 0.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.586 r_dihedral_angle_4_deg 28.761 r_dihedral_angle_3_deg 20.756 r_dihedral_angle_1_deg 7.597 r_scangle_it 3.169 r_scbond_it 1.896 r_angle_refined_deg 1.695 r_mcangle_it 1.59 r_angle_other_deg 0.948 r_mcbond_it 0.868 r_mcbond_other 0.129 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 695 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 37
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling