☰ Navigation Tabs
Crystal structure of a putative pyridoxine 5'-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G79 PDB ENTRY 1G79
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Tris/Maleate, PEG 10000, N,N-dimethyldodecylamine N-oxide, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.69 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.609 α = 90 b = 91.108 β = 90 c = 92.992 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 273 CCD ADSC QUANTUM 4 2003-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 29.48 100 21094 21094
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.64 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1G79 2.5 29.48 21067 19513 1535 99.91 0.20918 0.21281 0.20918 0.2092 0.26018 0.2573 RANDOM 36.303
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] 2.43 -2.48 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.709 r_dihedral_angle_4_deg 21.513 r_dihedral_angle_3_deg 19.291 r_dihedral_angle_1_deg 6.009 r_scangle_it 4.058 r_scbond_it 2.584 r_angle_refined_deg 2.007 r_mcangle_it 1.671 r_mcbond_it 0.971 r_symmetry_hbond_refined 0.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.709 r_dihedral_angle_4_deg 21.513 r_dihedral_angle_3_deg 19.291 r_dihedral_angle_1_deg 6.009 r_scangle_it 4.058 r_scbond_it 2.584 r_angle_refined_deg 2.007 r_mcangle_it 1.671 r_mcbond_it 0.971 r_symmetry_hbond_refined 0.429 r_nbtor_refined 0.317 r_nbd_refined 0.295 r_symmetry_vdw_refined 0.275 r_xyhbond_nbd_refined 0.195 r_chiral_restr 0.12 r_bond_refined_d 0.023 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3206 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing