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Crystal structure of the XplA heme domain in complex with imidazole and PEG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WIV PDB ENTRY 2WIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 50 mM magnesium chloride, 0.1 M imidazole/MES, pH 6.5, 30% PEG550 MME, PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.01 69.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.12 α = 90 b = 136.12 β = 90 c = 75.13 γ = 90
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 2011-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1 Diamond I04
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 2.3 43.04 100 28983 28983
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 2WIV 2.3 43.04 28983 28983 1534 100 0.20297 0.20297 0.20089 0.1996 0.24179 0.2393 RANDOM 43.021
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] -3.45 -3.45 6.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.69 r_dihedral_angle_4_deg 16.789 r_dihedral_angle_3_deg 15.192 r_dihedral_angle_1_deg 6.827 r_scangle_it 4.588 r_scbond_it 2.884 r_angle_refined_deg 1.885 r_mcangle_it 1.716 r_angle_other_deg 1.077 r_mcbond_it 0.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.69 r_dihedral_angle_4_deg 16.789 r_dihedral_angle_3_deg 15.192 r_dihedral_angle_1_deg 6.827 r_scangle_it 4.588 r_scbond_it 2.884 r_angle_refined_deg 1.885 r_mcangle_it 1.716 r_angle_other_deg 1.077 r_mcbond_it 0.914 r_mcbond_other 0.213 r_chiral_restr 0.11 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3056 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 64
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling