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N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FLM PDB ENTRY 1FLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 23% PEG 6000, 0.1M Tris, 0.2M sodium acetate, 19.8% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.33 47.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.868 α = 90 b = 83.038 β = 94.38 c = 40.239 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210r 2010-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 20 99.5 0.045 7.4 31712
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 1.69 100 0.196 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FLM 1.6 20 30085 1602 99.53 0.17146 0.17034 0.1697 0.19202 0.19 RANDOM 18.68
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] -0.58 -0.06 0.69 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.322 r_dihedral_angle_4_deg 16.16 r_dihedral_angle_3_deg 10.756 r_dihedral_angle_1_deg 5.563 r_scangle_it 2.805 r_scbond_it 1.684 r_mcangle_it 1.081 r_angle_refined_deg 1.058 r_mcbond_it 0.567 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.322 r_dihedral_angle_4_deg 16.16 r_dihedral_angle_3_deg 10.756 r_dihedral_angle_1_deg 5.563 r_scangle_it 2.805 r_scbond_it 1.684 r_mcangle_it 1.081 r_angle_refined_deg 1.058 r_mcbond_it 0.567 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1852 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 62
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling