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Crystal structure of protein af1124 from archaeoglobus fulgidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B3M PDB ID 2B3M (SEL-MET DERIVATIVE)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 AMMONIUM PHOSPHATE, TRIS HCL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.4 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.973 α = 90 b = 55.32 β = 93.36 c = 69.121 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 ADSC QUANTUM 315 2005-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97942 APS 19-ID
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 1.25 50 96.5 0.045 57.1 9 93720 90451 -3
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) 1.25 1.29 92.3 0.296 6.6 6.5
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 ID 2B3M (SEL-MET DERIVATIVE) 1.25 50 90428 90428 4536 96.47 0.14671 0.14671 0.14569 0.1554 0.16559 0.1685 RANDOM 17.145
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] -0.02 -0.03 0.4 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.15 r_dihedral_angle_4_deg 15.29 r_dihedral_angle_3_deg 11.964 r_dihedral_angle_1_deg 6.067 r_scangle_it 5.511 r_scbond_it 3.599 r_mcangle_it 2.517 r_angle_refined_deg 1.592 r_mcbond_it 1.586 r_rigid_bond_restr 1.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.15 r_dihedral_angle_4_deg 15.29 r_dihedral_angle_3_deg 11.964 r_dihedral_angle_1_deg 6.067 r_scangle_it 5.511 r_scbond_it 3.599 r_mcangle_it 2.517 r_angle_refined_deg 1.592 r_mcbond_it 1.586 r_rigid_bond_restr 1.578 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2678 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 5
Software Software Software Name Purpose AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling