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Crystal structure of the nitrocefin acyl-DD-peptidase from Actinomadura R39.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W79 PDB ENTRY 1W79
Crystallization Crystal Properties Matthews coefficient Solvent content 2.59 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.49 α = 90 b = 94.36 β = 94.58 c = 107.2 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 CCD MARRESEARCH MIRRORS 2004-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 2.4 40.8 86.6 0.1 9.5 2.9 69694 2 42.1
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 2.4 2.53 80.5 0.54 2.2 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1W79 2.4 19.94 2 69453 3524 86.3 0.22 0.22 0.2175 0.277 0.2743 RANDOM 43.6
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] -4.25 8.57 12.34 -8.08
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.2 c_scangle_it 2.53 c_mcangle_it 2.02 c_scbond_it 1.79 c_angle_deg 1.3 c_mcbond_it 1.23 c_improper_angle_d 0.84 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.2 c_scangle_it 2.53 c_mcangle_it 2.02 c_scbond_it 1.79 c_angle_deg 1.3 c_mcbond_it 1.23 c_improper_angle_d 0.84 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13394 Nucleic Acid Atoms Solvent Atoms 829 Heterogen Atoms 168
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling