☰ Navigation Tabs
Crystal structure of truncated FlgD (monoclinic form) from the human pathogen Helicobacter pylori (strain 26695)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 293 PEG 1500, succinic acid, sodium dihydrogen phosphate, glycine
Crystal Properties Matthews coefficient Solvent content 2.64 53.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.51 α = 90 b = 34 β = 98.9 c = 133.34 γ = 90
Symmetry Space Group P 1 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 PIXEL DECTRIS PILATUS 2M 2015-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.99988 ELETTRA 5.2R
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 2.8 76.58 94.8 4.9 2.7 16477
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 0.586
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ZZK 2.85 62.16 14806 798 93.55 0.22825 0.22678 0.25561 0.2733 RANDOM 69.249
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 -0.01 0.09 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.236 r_dihedral_angle_3_deg 16.936 r_long_range_B_refined 15.111 r_long_range_B_other 15.111 r_dihedral_angle_4_deg 12.436 r_scangle_other 9.096 r_mcangle_it 8.684 r_mcangle_other 8.682 r_dihedral_angle_1_deg 5.963 r_scbond_it 5.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.236 r_dihedral_angle_3_deg 16.936 r_long_range_B_refined 15.111 r_long_range_B_other 15.111 r_dihedral_angle_4_deg 12.436 r_scangle_other 9.096 r_mcangle_it 8.684 r_mcangle_other 8.682 r_dihedral_angle_1_deg 5.963 r_scbond_it 5.476 r_scbond_other 5.475 r_mcbond_it 5.403 r_mcbond_other 5.403 r_angle_refined_deg 1.488 r_angle_other_deg 1.425 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 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 4624 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling AMoRE phasing