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Crystal structure of a vinyl-4-reductase family protein (mj_1460) from methanocaldococcus jannaschii dsm at 2.40 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.1 277 NANODROP, 0.2M CaCl2, 20.0% PEG 3350, No Buffer, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 48.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.786 α = 90 b = 55.786 β = 90 c = 118.99 γ = 90
Symmetry Space Group P 43 21 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-01-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97879, 0.97908 SSRL BL11-1
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 2.3 29.748 99.9 0.084 0.084 6.6 6.9 8939
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 2.3 2.36 100 0.917 0.917 0.8 7.1 636
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.3 29.748 8895 421 99.93 0.221 0.221 0.219 0.2283 0.242 0.2482 RANDOM 54.04
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] 0.71 0.71 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.617 r_dihedral_angle_4_deg 31.953 r_dihedral_angle_3_deg 19.236 r_scangle_it 7.963 r_scbond_it 6.368 r_dihedral_angle_1_deg 6.22 r_mcangle_it 3.526 r_mcbond_it 2.223 r_angle_refined_deg 1.574 r_angle_other_deg 0.962
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.617 r_dihedral_angle_4_deg 31.953 r_dihedral_angle_3_deg 19.236 r_scangle_it 7.963 r_scbond_it 6.368 r_dihedral_angle_1_deg 6.22 r_mcangle_it 3.526 r_mcbond_it 2.223 r_angle_refined_deg 1.574 r_angle_other_deg 0.962 r_mcbond_other 0.446 r_symmetry_vdw_refined 0.375 r_metal_ion_refined 0.323 r_nbd_refined 0.226 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.189 r_nbd_other 0.187 r_symmetry_vdw_other 0.183 r_symmetry_metal_ion_refined 0.137 r_symmetry_hbond_refined 0.113 r_nbtor_other 0.093 r_chiral_restr 0.091 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1177 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 16
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling SHELXD phasing autoSHARP phasing