☰ Navigation Tabs
Crystal structure of human voltage-dependent anion channel 1 (hVDAC1) in P22121 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 36% PEG300, 0.1 M MES (pH 6.5), 0.1 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.95 58.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.7 α = 90 b = 84.96 β = 90 c = 146.23 γ = 90
Symmetry Space Group P 2 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 MARMOSAIC 225 mm CCD 2013-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 3.15 45.86 91.2 0.385 0.406 0.946 4.4 10.167 12096 -3 57.331
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.23 99.5 1.369 1.438 0.739 1.41 10.592
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 3EMN 3.15 45.86 11508 564 91.23 0.2673 0.2658 0.2676 0.2998 0.2993 RANDOM 66.266
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] -0.29 3.75 -3.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.109 r_dihedral_angle_3_deg 18.957 r_dihedral_angle_4_deg 12.841 r_dihedral_angle_1_deg 4.783 r_angle_refined_deg 1.043 r_chiral_restr 0.046 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4167 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing PHENIX refinement