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Structure of the soluble domain of the membrane protein TM1634 from Thermotoga maritima
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VKJ PDB ENTRY 2VKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 50% PEG200, 0.1 M NACITRATE PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.8 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.852 α = 90 b = 81.973 β = 101.41 c = 68.327 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 CCD 2006-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 1.8 50 99.2 0.08 17.9 3.2 51063 -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 1.8 1.84 99.6 0.57 3.2
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 2VKJ 1.79 66.96 48429 2595 99 0.243 0.241 0.2615 0.277 0.2979 RANDOM 32.58
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] -0.65 0.53 -0.26 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.159 r_dihedral_angle_3_deg 19.004 r_dihedral_angle_4_deg 14.489 r_scangle_it 7.553 r_dihedral_angle_1_deg 5.698 r_scbond_it 5.31 r_mcangle_it 2.514 r_mcbond_it 1.339 r_angle_refined_deg 1.31 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.159 r_dihedral_angle_3_deg 19.004 r_dihedral_angle_4_deg 14.489 r_scangle_it 7.553 r_dihedral_angle_1_deg 5.698 r_scbond_it 5.31 r_mcangle_it 2.514 r_mcbond_it 1.339 r_angle_refined_deg 1.31 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.236 r_symmetry_hbond_refined 0.221 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.101 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3384 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing