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Human methionine aminopeptidase type II in complex with D-methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BN5 PDB ENTRY 1BN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 18-23% t-butanol in 70 mM sodium citrate buffer, pH 5.3 to 5.6, 3 mM DTT
(DL-dithiothreitol), VAPOR DIFFUSION, SITTING DROP at 277K, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.67 41.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.727 α = 90 b = 98.938 β = 90 c = 100.628 γ = 90
Symmetry Space Group C 2 2 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 AREA DETECTOR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 CHESS F2
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 50 98.7 0.077 6.7 5 30241 3 27.33
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 2.11 93.2 0.405 14 2.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1BN5 2 50 28701 1516 98.7 0.19262 0.1913 0.198 0.21811 0.23 RANDOM 24.582
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] -0.04 0.03
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 1.968 p_angle_d 1.413 p_angle_deg 1.413 p_scbond_it 1.18 p_mcangle_it 0.824 p_mcbond_it 0.418 p_bond_d 0.009 p_planar_d p_hb_or_metal_coord p_plane_restr
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 1.968 p_angle_d 1.413 p_angle_deg 1.413 p_scbond_it 1.18 p_mcangle_it 0.824 p_mcbond_it 0.418 p_bond_d 0.009 p_planar_d p_hb_or_metal_coord p_plane_restr p_chiral_restr p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2782 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 11
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement CCP4 data scaling