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Crystal Structure of Fe-type NHase from Rhodococcus erythropolis AJ270
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AHJ PDB ENTRY 2AHJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 23% PEG 8000, 0.3M magnesium chloride, 0.1M TrisHCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.064 α = 90 b = 60.068 β = 125.15 c = 81.761 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 CCD MAR CCD 165 mm 2005-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 0.99 BSRF 3W1A
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 1.3 35.3 99.7 0.061 13.9 4.1 110924 110580 10.8
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 1.3 1.35 97.6 0.391 2.39 2.5 10756
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 2AHJ 1.3 35.3 110564 5531 99.68 0.131 0.129 0.1263 0.157 0.1543 RANDOM 14.118
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] 0.12 0.63 -0.24 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.647 r_dihedral_angle_4_deg 20.589 r_dihedral_angle_3_deg 10.694 r_sphericity_free 8.935 r_sphericity_bonded 6.515 r_dihedral_angle_1_deg 5.702 r_scangle_it 3.73 r_scbond_it 2.839 r_mcangle_it 2.22 r_angle_refined_deg 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.647 r_dihedral_angle_4_deg 20.589 r_dihedral_angle_3_deg 10.694 r_sphericity_free 8.935 r_sphericity_bonded 6.515 r_dihedral_angle_1_deg 5.702 r_scangle_it 3.73 r_scbond_it 2.839 r_mcangle_it 2.22 r_angle_refined_deg 1.71 r_mcbond_it 1.671 r_rigid_bond_restr 1.644 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.211 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.13 r_metal_ion_refined 0.108 r_symmetry_metal_ion_refined 0.026 r_bond_refined_d 0.017 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3199 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 49
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing