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Crystal Structure of a Trapped Phosphate-Intermediate in Vanadium Apochloroperoxidase Catalyzing a Dephosphorylation Reaction
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VNS PDB ENTRY 1VNS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 3 micro-l of protein solution (5mg/ml in 5mM MOPS, pH 7.5), 3 micro-l precipitating buffer (1.7M ammonium sulfate, 0.1M Tris-HCl, pH 8.0, 0.3 micro-l 10mM cysteine-HCl) , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 48.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.06 α = 90 b = 128.06 β = 90 c = 103.31 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors 1998-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 50 99.1 0.062 0.062 8.2 1.8 101188 100278 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.53 96 0.317 0.317 3.5 1.8 5046
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VNS 1.5 14.9 96066 95202 5076 100 0.17391 0.17283 0.1735 0.19391 RANDOM 17.863
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 -0.08 -0.15 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.558 r_dihedral_angle_4_deg 14.128 r_dihedral_angle_3_deg 11.81 r_dihedral_angle_1_deg 9.235 r_scangle_it 2.429 r_scbond_it 1.643 r_angle_refined_deg 1.229 r_mcangle_it 1.142 r_mcbond_it 0.715 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.558 r_dihedral_angle_4_deg 14.128 r_dihedral_angle_3_deg 11.81 r_dihedral_angle_1_deg 9.235 r_scangle_it 2.429 r_scbond_it 1.643 r_angle_refined_deg 1.229 r_mcangle_it 1.142 r_mcbond_it 0.715 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.212 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.183 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4498 Nucleic Acid Atoms Solvent Atoms 796 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling MOLREP phasing