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Crystal Structure of Native-ORF134
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z44 PDB ENTRY 2Z44
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.4M Na acetate, 0.1M Na cacodylate
, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.92 74.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.794 α = 90 b = 93.794 β = 90 c = 410.222 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2005-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.9200 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.97 50 99.3 0.088 37069 90.4
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) 2.97 3.08 95.1 0.726
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Z44 2.97 50 37069 1955 99.7 0.24961 0.24814 0.2361 0.27675 0.2666 RANDOM 71.089
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] 0.44 0.44 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_dihedral_angle_3_deg 21.309 r_dihedral_angle_4_deg 18.892 r_dihedral_angle_1_deg 5.489 r_scangle_it 2.007 r_angle_refined_deg 1.268 r_scbond_it 1.105 r_mcangle_it 1.067 r_mcbond_it 0.587 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_dihedral_angle_3_deg 21.309 r_dihedral_angle_4_deg 18.892 r_dihedral_angle_1_deg 5.489 r_scangle_it 2.007 r_angle_refined_deg 1.268 r_scbond_it 1.105 r_mcangle_it 1.067 r_mcbond_it 0.587 r_nbtor_refined 0.301 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.181 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 5347 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing