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crystal structure of Human Methionine aminopeptidase (HsMetAP1b) in complex with AN-P2-5H-06
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 0.1M Bistris pH-6.2, 19% PEG 3350, 5% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.42 49.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.573 α = 90 b = 77.251 β = 91.54 c = 48.623 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2019-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.95360 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.29 47.56 99.7 0.047 0.051 0.019 0.999 17.9 6.6 87661
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.29 1.31 98.5 0.972 1.065 0.426 0.856 6.1
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 2B3H 1.29 40.53 82898 4192 98.98 0.1645 0.1626 0.1703 0.1998 0.2055 RANDOM 25.322
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] 0.15 -0.35 -0.35 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.378 r_dihedral_angle_4_deg 14.154 r_dihedral_angle_3_deg 12.89 r_dihedral_angle_1_deg 6.987 r_rigid_bond_restr 6.589 r_angle_refined_deg 2.145 r_angle_other_deg 1.639 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.378 r_dihedral_angle_4_deg 14.154 r_dihedral_angle_3_deg 12.89 r_dihedral_angle_1_deg 6.987 r_rigid_bond_restr 6.589 r_angle_refined_deg 2.145 r_angle_other_deg 1.639 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2396 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction Coot model building XDS data reduction