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PrnB D-tryptophan complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V7J PDB ENTRY 2V7J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.9 57.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.265 α = 90 b = 79.546 β = 103.42 c = 92.309 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.75 37 98 0.07 12 3 48852
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 1.75 1.84 96 0.67 2 3.8
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 2V7J 1.7 89.8 48852 2630 97.5 0.185 0.183 0.1846 0.206 0.2063 RANDOM 32.72
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] 0.3 0.19 -0.25 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.364 r_dihedral_angle_4_deg 18.238 r_dihedral_angle_3_deg 12.222 r_dihedral_angle_1_deg 4.571 r_scangle_it 2.58 r_scbond_it 1.427 r_angle_refined_deg 1.112 r_mcangle_it 0.887 r_mcbond_it 0.588 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.364 r_dihedral_angle_4_deg 18.238 r_dihedral_angle_3_deg 12.222 r_dihedral_angle_1_deg 4.571 r_scangle_it 2.58 r_scbond_it 1.427 r_angle_refined_deg 1.112 r_mcangle_it 0.887 r_mcbond_it 0.588 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.128 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.072 r_bond_refined_d 0.009 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 2698 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling