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Crystal structure of methanol dehydrogenase from Hyphomicrobium denitrificans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 PEG3350, potassium thiocyanate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.2 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 291.32 α = 90 b = 63.999 β = 105.74 c = 109.941 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 Bruker DIP-6040 2005-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.49 44.6 99.6 68299 68299
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 99.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.49 44.6 68299 61400 6898 99.61 0.192 0.15854 0.14863 0.1615 0.24687 0.1612 RANDOM 33.61
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] -2.34 -0.97 2.47 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.066 r_dihedral_angle_4_deg 18.456 r_dihedral_angle_3_deg 18.191 r_dihedral_angle_1_deg 8.105 r_scangle_it 4.428 r_scbond_it 3.014 r_angle_refined_deg 2.328 r_mcangle_it 1.874 r_mcbond_it 1.135 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.066 r_dihedral_angle_4_deg 18.456 r_dihedral_angle_3_deg 18.191 r_dihedral_angle_1_deg 8.105 r_scangle_it 4.428 r_scbond_it 3.014 r_angle_refined_deg 2.328 r_mcangle_it 1.874 r_mcbond_it 1.135 r_nbtor_refined 0.325 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.245 r_symmetry_hbond_refined 0.198 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.162 r_metal_ion_refined 0.057 r_bond_refined_d 0.027 r_gen_planes_refined 0.01 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_other r_symmetry_vdw_other 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 15689 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing