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Crystal structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FVP PDB ENTRY 3FVP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2M NACL, 0.1 M HEPES PH 7.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.99 37.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.121 α = 90 b = 77.021 β = 103.58 c = 64.443 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 120 PIXEL DECTRIS PILATUS 6M 2011-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 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 1.76 48.6 97.5 0.11 7.9 3.3 57590
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 1.76 1.86 97.5 0.67 1.6 3.3
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 PDB ENTRY 3FVP 1.76 48.6 53023 2791 96.92 0.19768 0.19508 0.1954 0.24749 0.2484 RANDOM 16.516
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] -0.56 -0.43 0.66 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.871 r_dihedral_angle_4_deg 14.907 r_dihedral_angle_3_deg 14.385 r_dihedral_angle_1_deg 6.472 r_angle_refined_deg 2.136 r_chiral_restr 0.137 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.871 r_dihedral_angle_4_deg 14.907 r_dihedral_angle_3_deg 14.385 r_dihedral_angle_1_deg 6.472 r_angle_refined_deg 2.136 r_chiral_restr 0.137 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4580 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction SADABS data scaling PHASER phasing