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Crystal structure of a pyridoxamine 5'-phosphate oxidase-related fmn-binding protein (jann_0254) from jannaschia sp. ccs1 at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 NANODROP, 1.6M (NH4)2SO4, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.88 α = 90 b = 68.51 β = 90 c = 111.92 γ = 90
Symmetry Space Group P 21 21 21
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) 2007-02-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162, 0.97922, 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 1.6 28.94 95 0.04 12.43 46954 24.807
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 1.6 1.66 84.4 0.299 2.4 7931
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 1.6 28.94 46899 2370 99.18 0.181 0.181 0.178 0.1882 0.221 0.225 RANDOM 18.781
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] 0.1 1.5 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.173 r_dihedral_angle_4_deg 17.228 r_dihedral_angle_3_deg 11.972 r_dihedral_angle_1_deg 6.219 r_scangle_it 5.671 r_scbond_it 4.34 r_mcangle_it 2.886 r_mcbond_it 2.174 r_angle_refined_deg 1.622 r_angle_other_deg 0.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.173 r_dihedral_angle_4_deg 17.228 r_dihedral_angle_3_deg 11.972 r_dihedral_angle_1_deg 6.219 r_scangle_it 5.671 r_scbond_it 4.34 r_mcangle_it 2.886 r_mcbond_it 2.174 r_angle_refined_deg 1.622 r_angle_other_deg 0.877 r_mcbond_other 0.597 r_symmetry_vdw_refined 0.224 r_symmetry_vdw_other 0.222 r_symmetry_hbond_refined 0.215 r_nbd_refined 0.201 r_nbd_other 0.196 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.089 r_nbtor_other 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2693 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 91
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing SHARP phasing