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Crystal structure of non-symbiotic plant hemoglobin from rice, B10 mutant F40L
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D8U 1D8U.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 1.9M Ammonium Phosphate, 10mM Potassium Phosphate, 20% Sucrose, 3% Dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.46 64.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.286 α = 90 b = 125.286 β = 90 c = 56.25 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV OSMIC CONFOCAL 2002-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2 111.803 0.065 34568 32270
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.052 1507
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 1D8U.pdb 2.3 20 22818 22761 1149 99.75 0.203 0.203 0.201 0.2088 0.247 0.2524 RANDOM 42.47
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] 1.05 0.52 1.05 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.636 r_scangle_it 3.544 r_scbond_it 2.1 r_mcangle_it 1.791 r_angle_refined_deg 1.383 r_mcbond_it 0.949 r_angle_other_deg 0.853 r_symmetry_hbond_refined 0.366 r_nbd_other 0.236 r_symmetry_vdw_other 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.636 r_scangle_it 3.544 r_scbond_it 2.1 r_mcangle_it 1.791 r_angle_refined_deg 1.383 r_mcbond_it 0.949 r_angle_other_deg 0.853 r_symmetry_hbond_refined 0.366 r_nbd_other 0.236 r_symmetry_vdw_other 0.228 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.219 r_symmetry_vdw_refined 0.151 r_nbtor_other 0.09 r_chiral_restr 0.077 r_metal_ion_refined 0.017 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2447 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 110
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CNS phasing