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Crystal structure of a putative flavin reductase (ycdh, hs_1225) from haemophilus somnus 129pt at 1.06 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 NANODROP, 2.0M Ammonium sulfate, 0.1M Sodium acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.75 29.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.02 α = 90 b = 38.85 β = 115.63 c = 48.44 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-07-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97925, 0.97898 SSRL BL11-1
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 1.06 23.402 98.9 0.07 6.34 54635 6.164
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) 1.06 1.1 97.8 0.678 1.34 9171
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 1.06 23.402 54635 2771 99.62 0.143 0.143 0.141 0.1502 0.17 0.1754 RANDOM 9.358
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] -0.15 0.11 0.16 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.212 r_dihedral_angle_4_deg 18.543 r_sphericity_free 13.401 r_dihedral_angle_3_deg 11.103 r_dihedral_angle_1_deg 7.287 r_sphericity_bonded 5.84 r_scangle_it 3.523 r_mcangle_it 3.08 r_scbond_it 2.632 r_mcbond_it 2.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.212 r_dihedral_angle_4_deg 18.543 r_sphericity_free 13.401 r_dihedral_angle_3_deg 11.103 r_dihedral_angle_1_deg 7.287 r_sphericity_bonded 5.84 r_scangle_it 3.523 r_mcangle_it 3.08 r_scbond_it 2.632 r_mcbond_it 2.236 r_angle_refined_deg 1.667 r_rigid_bond_restr 1.44 r_angle_other_deg 0.993 r_mcbond_other 0.832 r_symmetry_vdw_other 0.275 r_nbd_refined 0.247 r_nbd_other 0.21 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.106 r_nbtor_other 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1178 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing