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Crystal structure of Hma (MmaA4) from Mycobacterium tuberculosis, apo-form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KP9 pdb entry 1KP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 285 4-28% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K
Crystal Properties Matthews coefficient Solvent content 2.76 55.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.715 α = 90 b = 56.715 β = 90 c = 206.22 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 CCD MARRESEARCH Toroidal mirror 2004-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931000 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 44.3 97.5 0.1 3.8 9.7 22776 22776 42.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 100 0.186 3.7 10 3315
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 1KP9 2.1 30 21535 21535 1173 97.05 0.19734 0.19734 0.19546 0.2041 0.23226 0.241 RANDOM 65.44
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 30.047 r_dihedral_angle_4_deg 23.723 r_dihedral_angle_3_deg 13.795 r_dihedral_angle_1_deg 5.854 r_scangle_it 3.95 r_scbond_it 2.788 r_angle_refined_deg 1.736 r_mcangle_it 1.636 r_mcbond_it 1.176 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.047 r_dihedral_angle_4_deg 23.723 r_dihedral_angle_3_deg 13.795 r_dihedral_angle_1_deg 5.854 r_scangle_it 3.95 r_scbond_it 2.788 r_angle_refined_deg 1.736 r_mcangle_it 1.636 r_mcbond_it 1.176 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.211 r_chiral_restr 0.132 r_xyhbond_nbd_refined 0.123 r_symmetry_vdw_refined 0.111 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2218 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing