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Crystal structure of Streptococcus pneumoniae dihydrofolate reductase - Sp9 mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZDR PDB entry 1ZDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 298 1M Lithium chloride, 0.1M Sodium citrate pH 4.0, 20% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.838 α = 90 b = 93.639 β = 90 c = 71.367 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 93 CCD RIGAKU SATURN 944+ 2008-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.95 40 92.6 0.102 5.6 2.34 28610 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) 1.95 2.02 92.6 0.21 2.4 1.41
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 1ZDR 1.95 20 28610 28610 1424 92.6 0.237 0.237 0.2375 0.274 0.2733 RANDOM
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] 8.182 -3.6 -4.581
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 4.484 c_scbond_it 3.577 c_mcangle_it 3.232 c_mcbond_it 2.521 c_angle_deg 1.52 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 4.484 c_scbond_it 3.577 c_mcangle_it 3.232 c_mcbond_it 2.521 c_angle_deg 1.52 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2750 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 162
Software Software Software Name Purpose CrystalClear data collection PHASER phasing CNS refinement CrystalClear data reduction CrystalClear data scaling