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CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-like family protein (NPUN_R6570) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.80 A RESOLUTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 277 0.2M NaCl, 40.0% PEG-300, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.38 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.646 α = 90 b = 103.646 β = 90 c = 109.695 γ = 120
Symmetry Space Group P 63 2 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 ADSC QUANTUM 315 Flat mirror (vertical focusing) 2006-07-02 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.979197,0.918370 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 29.921 100 0.117 0.117 4.8 10.3 32823
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 100 0.946 0.946 0.8 10.6 2377
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.8 29.921 32793 1663 99.99 0.178 0.177 0.1868 0.204 0.2121 RANDOM 25.749
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] -0.55 -0.27 -0.55 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.584 r_dihedral_angle_4_deg 13.334 r_dihedral_angle_3_deg 13.209 r_scangle_it 7.245 r_dihedral_angle_1_deg 6.242 r_scbond_it 5.215 r_mcangle_it 3.393 r_mcbond_it 2.36 r_angle_refined_deg 1.496 r_angle_other_deg 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.584 r_dihedral_angle_4_deg 13.334 r_dihedral_angle_3_deg 13.209 r_scangle_it 7.245 r_dihedral_angle_1_deg 6.242 r_scbond_it 5.215 r_mcangle_it 3.393 r_mcbond_it 2.36 r_angle_refined_deg 1.496 r_angle_other_deg 0.88 r_mcbond_other 0.568 r_nbd_refined 0.22 r_symmetry_vdw_other 0.22 r_nbd_other 0.199 r_symmetry_vdw_refined 0.188 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.158 r_nbtor_other 0.088 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2262 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 53
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling SHELXD phasing SHARP phasing