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Crystal structure of LpxH with manganese from Pseudomonas aeruginosa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 293 0.2M L-Proline, 0.1M HEPES pH 7.6, 8.5% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.937 α = 90 b = 108.862 β = 92.68 c = 51.555 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 100 CCD RAYONIX MX225HE 2011-02-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000, 1.8925 SPring-8 BL41XU
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 1.65 50 100 0.075 20.4 6.7 64565
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 1.65 1.71 100 0.485 2.23 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.65 29.23 61172 3300 99.68 0.15288 0.15162 0.1635 0.17662 0.1861 RANDOM 21.893
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] 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.629 r_dihedral_angle_4_deg 15.669 r_dihedral_angle_3_deg 11.586 r_long_range_B_refined 6.612 r_long_range_B_other 6.357 r_scangle_other 5.477 r_dihedral_angle_1_deg 5.467 r_scbond_it 3.605 r_scbond_other 3.599 r_mcangle_it 2.671
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.629 r_dihedral_angle_4_deg 15.669 r_dihedral_angle_3_deg 11.586 r_long_range_B_refined 6.612 r_long_range_B_other 6.357 r_scangle_other 5.477 r_dihedral_angle_1_deg 5.467 r_scbond_it 3.605 r_scbond_other 3.599 r_mcangle_it 2.671 r_mcangle_other 2.671 r_mcbond_it 1.965 r_mcbond_other 1.963 r_angle_refined_deg 1.403 r_angle_other_deg 0.971 r_chiral_restr 0.052 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3942 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELXCD phasing