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Crystal structure of carbonmonoxy human cytoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V5H PDB ENTRY 1V5H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch 8 293 20% PEG 3350, 20mM ammonium acetate, 5mM sodium dithionite, pH 8.0, batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.73 29.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.198 α = 90 b = 43.977 β = 90 c = 94.019 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 ADSC QUANTUM 315 K-B mirrors 2007-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.6 50 98.6 0.104 0.112 16.31 4892 -3 36.121
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.69 100 0.498 0.54 4.5
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 1V5H 2.6 19.92 4877 246 98.6 0.215 0.215 0.2109 0.248 0.2557 RANDOM 36.5
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] -7.04 -2.08 9.12
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.7 c_scangle_it 6.48 c_scbond_it 5.04 c_mcangle_it 4.96 c_mcbond_it 3.42 c_angle_deg 1.7 c_improper_angle_d 1.29 c_bond_d 0.014 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.7 c_scangle_it 6.48 c_scbond_it 5.04 c_mcangle_it 4.96 c_mcbond_it 3.42 c_angle_deg 1.7 c_improper_angle_d 1.29 c_bond_d 0.014 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1264 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 45
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction BSS data collection DENZO data reduction SCALEPACK data scaling