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Crystal structure of Synechococcus sp. PCC 7002 globin at cryogenic temperature with heme modification
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RTX PDB ENTRY 1RTX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 7% glycerol, 2 M ammonium sulfate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.791 α = 90 b = 68.791 β = 90 c = 156.059 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS PILATUS 6M Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification 2012-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.10 NSLS X25
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 1.444 50 98.9 0.087 11 13.2 67233 67233
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 1.444 1.48 95.5 0.382 4.544 5.9 3198
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 1RTX 1.444 41.49 67144 67144 3410 98.73 0.1742 0.1742 0.1732 0.1825 0.1937 0.2018 RANDOM 17.0445
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.518 r_dihedral_angle_4_deg 15.928 r_dihedral_angle_3_deg 13.77 r_dihedral_angle_1_deg 5.121 r_angle_refined_deg 1.717 r_mcangle_it 1.415 r_mcbond_it 1.01 r_mcbond_other 1.003 r_angle_other_deg 0.661 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.518 r_dihedral_angle_4_deg 15.928 r_dihedral_angle_3_deg 13.77 r_dihedral_angle_1_deg 5.121 r_angle_refined_deg 1.717 r_mcangle_it 1.415 r_mcbond_it 1.01 r_mcbond_other 1.003 r_angle_other_deg 0.661 r_chiral_restr 0.072 r_gen_planes_refined 0.018 r_bond_refined_d 0.016 r_gen_planes_other 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2901 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 169
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction