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An oxidized tryptophan facilitates copper-binding in Methylococcus capsulatus secreted protein MopE. The structure of wild-type MopE to 1.35AA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VOX PDB ENTRY 2VOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 36-45% AMMONIUM SULFATE, 0.1 M HEPES PH 7.25-7.75
Crystal Properties Matthews coefficient Solvent content 2.2 43.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.99 α = 90 b = 88.57 β = 90 c = 101.43 γ = 90
Symmetry Space Group I 2 2 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A ESRF BM1A
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 1.35 28.3 98.5 0.04 8.6 5.2 71009 14.1
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 1.35 1.42 97.3 0.05 1.6 5.2
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 2VOX 1.35 28.3 67423 3583 98.3 0.194 0.193 0.1895 0.211 0.2087 RANDOM 16.68
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] 0.23 0.38 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.77 r_dihedral_angle_4_deg 19.687 r_scbond_it 12.181 r_dihedral_angle_3_deg 10.553 r_scangle_it 8.831 r_dihedral_angle_1_deg 6.846 r_mcangle_it 3.969 r_mcbond_it 3.527 r_angle_refined_deg 1.141 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.77 r_dihedral_angle_4_deg 19.687 r_scbond_it 12.181 r_dihedral_angle_3_deg 10.553 r_scangle_it 8.831 r_dihedral_angle_1_deg 6.846 r_mcangle_it 3.969 r_mcbond_it 3.527 r_angle_refined_deg 1.141 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.227 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 2234 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing