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Crystal Structure of Cryptosporidium parvum malate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 15% PEG4K, 0.2M NH4oAC, Nacitrate pH 5.6, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.74 55.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.887 α = 90 b = 171.887 β = 90 c = 135.606 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2006-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 20 99.9 0.117 0.075 14.6 5 227472 227351
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 99.9 0.864 0.737 1.911 4.7 22734
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 (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 1GUY 2.2 19.83 215627 11391 99.96 0.20048 0.20048 0.19799 0.1949 0.24747 0.2426 RANDOM 34.344
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.965 r_dihedral_angle_4_deg 25.429 r_dihedral_angle_3_deg 17.785 r_dihedral_angle_1_deg 5.29 r_scangle_it 2.839 r_scbond_it 1.817 r_angle_refined_deg 1.516 r_mcangle_it 1.085 r_mcbond_it 0.628 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.965 r_dihedral_angle_4_deg 25.429 r_dihedral_angle_3_deg 17.785 r_dihedral_angle_1_deg 5.29 r_scangle_it 2.839 r_scbond_it 1.817 r_angle_refined_deg 1.516 r_mcangle_it 1.085 r_mcbond_it 0.628 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.125 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28040 Nucleic Acid Atoms Solvent Atoms 1337 Heterogen Atoms 588
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing