☰ Navigation Tabs
Structure of Hypothetical protein from Leishmania major
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other low resolution MAD structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 273 1.0 ul protein 8.2 mg/ml
1.0 ul crystallization buffer 2.8 M Na Malonate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties Matthews coefficient Solvent content 1.8 31.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.199 α = 90 b = 64.607 β = 90 c = 72.559 γ = 90
Symmetry Space Group P 21 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 100 CCD ADSC QUANTUM 210 2004-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-3 SSRL BL11-3
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 1.6 50 95.3 0.041 10.068 2.9 19933 18997
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 1.6 1.65 94.6 0.693 1.603
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 low resolution MAD structure 1.602 29.514 18995 18995 974 94.913 0.187 0.187 0.185 0.1999 0.2294 0.199 random 19.803
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] 0.517 0.395 -0.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.257 r_dihedral_angle_4_deg 16.553 r_dihedral_angle_3_deg 14.551 r_dihedral_angle_1_deg 6.669 r_scangle_it 5.175 r_scbond_it 3.936 r_scangle_other 2.573 r_mcbond_it 2.559 r_mcangle_it 2.506 r_angle_refined_deg 1.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.257 r_dihedral_angle_4_deg 16.553 r_dihedral_angle_3_deg 14.551 r_dihedral_angle_1_deg 6.669 r_scangle_it 5.175 r_scbond_it 3.936 r_scangle_other 2.573 r_mcbond_it 2.559 r_mcangle_it 2.506 r_angle_refined_deg 1.927 r_scbond_other 1.77 r_mcangle_other 1.228 r_angle_other_deg 0.917 r_mcbond_other 0.581 r_symmetry_hbond_refined 0.314 r_symmetry_vdw_other 0.273 r_nbd_refined 0.22 r_nbd_other 0.209 r_symmetry_vdw_refined 0.201 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.118 r_nbtor_other 0.088 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1297 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction MOLREP phasing REFMAC refinement