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Precursor of Protealysin, Metalloproteinase from Serratia proteamaculans.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NPC PDB ENTRY 1NPC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 THE HANGING-DROP VAPOR DIFFUSION METHOD AGAINST A PRECIPITANT SOLUTION OF 15% PEG MME 2000, 0.2M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6. DROPLETS CONTAINED 3 MKL OF 10 MG/ML PROTEIN SOLUTION AND 1.5 MKL PRECIPITANT SOLUTION WITH 0.06% BETA-OCTIL-D-GLUCOPYRANOSIDE IN THE SAME BUFFER
Crystal Properties Matthews coefficient Solvent content 2.15 42.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.76 α = 90 b = 78.65 β = 90 c = 59.28 γ = 90
Symmetry Space Group P 21 21 2
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 MARRESEARCH 2007-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 KURCHATOV SNC K4.4
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 52.6 90.9 0.03 26.9 2.82 28551 2 26.2
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 2 78.6 0.09 11.07 2.6
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 1NPC 1.821 52.63 27076 1448 94.2 0.17141 0.16984 0.176 0.20205 0.208 RANDOM 12.3
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] -0.183 -0.269 0.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.294 r_dihedral_angle_4_deg 14.787 r_dihedral_angle_3_deg 12.484 r_dihedral_angle_1_deg 5.096 r_scangle_it 1.629 r_angle_other_deg 1.266 r_scbond_it 1.168 r_angle_refined_deg 1.039 r_mcangle_it 0.666 r_mcbond_it 0.562
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.294 r_dihedral_angle_4_deg 14.787 r_dihedral_angle_3_deg 12.484 r_dihedral_angle_1_deg 5.096 r_scangle_it 1.629 r_angle_other_deg 1.266 r_scbond_it 1.168 r_angle_refined_deg 1.039 r_mcangle_it 0.666 r_mcbond_it 0.562 r_symmetry_vdw_other 0.219 r_nbd_refined 0.197 r_nbd_other 0.178 r_symmetry_vdw_refined 0.172 r_nbtor_refined 0.166 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.112 r_mcbond_other 0.093 r_nbtor_other 0.08 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other 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 2507 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction XDS data scaling BALBES phasing MOLREP phasing REFMAC refinement