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Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CBF PDB ENTRY 1CBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 0.1M Hepes pH 7.5, 10% isopropanol, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.66 53.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.517 α = 90 b = 84.517 β = 90 c = 144.637 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 CCD MARMOSAIC 225 mm CCD 2007-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.117 SRS PX10.1
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 2 42.26 100 0.068 0.068 19.2 9.8 39472 39472 33.23
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 2 2.11 100 0.62 0.62 3.3 8.5 5720
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1CBF 2 40.56 37436 37425 1979 99.97 0.18875 0.18694 0.186 0.2219 0.2209 RANDOM 36.858
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.865 r_dihedral_angle_4_deg 16.904 r_dihedral_angle_3_deg 12.855 r_dihedral_angle_1_deg 6.07 r_scangle_it 2.947 r_scbond_it 1.794 r_mcangle_it 1.362 r_angle_refined_deg 1.344 r_mcbond_it 0.754 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.865 r_dihedral_angle_4_deg 16.904 r_dihedral_angle_3_deg 12.855 r_dihedral_angle_1_deg 6.07 r_scangle_it 2.947 r_scbond_it 1.794 r_mcangle_it 1.362 r_angle_refined_deg 1.344 r_mcbond_it 0.754 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3435 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 52
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling