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Haemophilus influenzae LpoA: Monoclinic form (Mon2) with 2 molecules per a.u.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CKM 3CKM, 4P29 experimental model PDB 4P29 3CKM, 4P29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 One microliter of concentrated protein (33 mg/ml in 150 mm NaCl, 50 mm Tris-HCl, ph 8.0) and one microliter precipitant (8% polyethylene glycol 4000, 0.1 m sodium acetate trihydrate, ph 4.6) and 0.2 microliter 30% xylitol. Cryoprotectant: precipitant solution containing 15% glycerol.
Crystal Properties Matthews coefficient Solvent content 3.11 60.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.935 α = 90 b = 72.695 β = 94.42 c = 120.572 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 125 CCD RAYONIX MX-300 MONOCHROMATOR 2009-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07806 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.49 100 87.09 0.087 0.107 0.061 0.9 11.9 2.66 45736 39.5642078485
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.53 65.1 0.513 0.647 0.389 0.635 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3CKM, 4P29 2.6 42.341 1.35 72309 3153 81.82 0.2247 0.2233 0.2256 0.2568 0.257 73.3186
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.132 f_angle_d 0.542 f_chiral_restr 0.039 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8410 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling