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Structure of human Bcl-2 in complex with PUMA BH3 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 284 from 0.2M MgCl2, 25% PegMME 2k, 0.1M Na Acetate buffer pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.05 40.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.135 α = 90 b = 54.95 β = 90 c = 84.725 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2008-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979 ESRF ID29
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 1.8 50 75 0.111 7.1 3.5 13577
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 1.8 1.86 16.7 0.534 1.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2yxj 1.9 20 12321 647 84.42 0.1713 0.169 0.2163 0.2272 RANDOM 29.333
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] 0.07 -1.77 1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.675 r_dihedral_angle_4_deg 18.04 r_dihedral_angle_3_deg 16.779 r_dihedral_angle_1_deg 5.243 r_angle_refined_deg 1.485 r_angle_other_deg 1.08 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.675 r_dihedral_angle_4_deg 18.04 r_dihedral_angle_3_deg 16.779 r_dihedral_angle_1_deg 5.243 r_angle_refined_deg 1.485 r_angle_other_deg 1.08 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1270 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing