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Crystal structure of a putative nad(p)h:fmn oxidoreductase (pg0310) from porphyromonas gingivalis w83 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 2.0000M (NH4)2SO4, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.06 α = 90 b = 112.06 β = 90 c = 68.3 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) 2008-11-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97870,0.97833 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 1.7 29.161 99.5 0.066 14.75 48232 -3 20.057
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 1.7 1.76 98 0.735 1.8
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 (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 1.7 29.161 48177 2445 99.72 0.146 0.145 0.1515 0.172 0.1736 RANDOM 21.752
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] -0.53 -0.53 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.873 r_dihedral_angle_3_deg 11.085 r_dihedral_angle_4_deg 10.057 r_dihedral_angle_1_deg 5.773 r_scangle_it 5.361 r_scbond_it 3.753 r_mcangle_it 2.343 r_mcbond_it 1.829 r_angle_refined_deg 1.428 r_angle_other_deg 0.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.873 r_dihedral_angle_3_deg 11.085 r_dihedral_angle_4_deg 10.057 r_dihedral_angle_1_deg 5.773 r_scangle_it 5.361 r_scbond_it 3.753 r_mcangle_it 2.343 r_mcbond_it 1.829 r_angle_refined_deg 1.428 r_angle_other_deg 0.966 r_mcbond_other 0.491 r_symmetry_vdw_refined 0.396 r_symmetry_vdw_other 0.392 r_nbd_refined 0.309 r_nbd_other 0.21 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_other 0.118 r_chiral_restr 0.084 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2805 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing