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Crystal structure of a truncated version of the phage lamda protein gpD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C5E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 Tris-HCl, PEG 4000, Mg acetate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.53 51.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.186 α = 90 b = 99.044 β = 119 c = 59.321 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 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 0.98 NSLS X9B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 25 23.5
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 1C5E 1.85 19.59 46980 4712 93.7 0.191 0.191 0.1911 0.232 0.2321 RANDOM 28.8
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] -1.94 1.52 0.64 1.29
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 3.35 c_mcangle_it 2.56 c_scbond_it 2.52 c_mcbond_it 1.83 c_angle_deg 1.3 c_improper_angle_d 0.9 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 3.35 c_mcangle_it 2.56 c_scbond_it 2.52 c_mcbond_it 1.83 c_angle_deg 1.3 c_improper_angle_d 0.9 c_bond_d 0.008 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_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4146 Nucleic Acid Atoms Solvent Atoms 685 Heterogen Atoms
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing