X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PG4pdb entry 1PG4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52876-15% PEG 8000, 9-13% ethylene glycol, 50 mM BTP, 1 mM CoA, 1 mM Propyl-AMP, 1 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.1241.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.915α = 90
b = 143.076β = 90.97
c = 71.379γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDCUSTOM-MADE2003-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.10NSLSX12C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.23096.90.04712.459117
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2892.60.1485617

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1PG42.23058947298096.880.1680.1660.211RANDOM24.898
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]
-0.76-1.25-0.351.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.359
r_dihedral_angle_4_deg18.778
r_dihedral_angle_3_deg14.105
r_dihedral_angle_1_deg6.109
r_scangle_it2.766
r_scbond_it1.743
r_angle_refined_deg1.349
r_mcangle_it1.049
r_mcbond_it0.634
r_symmetry_hbond_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.359
r_dihedral_angle_4_deg18.778
r_dihedral_angle_3_deg14.105
r_dihedral_angle_1_deg6.109
r_scangle_it2.766
r_scbond_it1.743
r_angle_refined_deg1.349
r_mcangle_it1.049
r_mcbond_it0.634
r_symmetry_hbond_refined0.312
r_nbtor_refined0.303
r_symmetry_vdw_refined0.197
r_nbd_refined0.196
r_xyhbond_nbd_refined0.133
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9805
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms148

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction