X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M7Gpdb id 1M7G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP295reservoir: 18-20% PEG 3350, 0.25 M calcium acetate protein solution: 5-8 mg/ml protein, 3 mM APS, 5 mM MgCl2, 50 mM Tris pH 7.5, 50 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2846

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.19α = 90
b = 69.03β = 116.61
c = 150.61γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2004-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM0.9594APS22-BM

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.051083.60.0950.08212.43.7121588101698
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)RedundancyNumber Unique Reflections (All)
2.052.192.80.3010.244.362.57260

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 id 1M7G2.05101010661010797.470.2230.2170.282RANDOM27.759
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]
0.62-0.02-0.650.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.362
r_dihedral_angle_4_deg18.209
r_dihedral_angle_3_deg16.318
r_dihedral_angle_1_deg5.807
r_scangle_it2.403
r_angle_refined_deg1.729
r_scbond_it1.575
r_mcangle_it1.021
r_mcbond_it0.611
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.362
r_dihedral_angle_4_deg18.209
r_dihedral_angle_3_deg16.318
r_dihedral_angle_1_deg5.807
r_scangle_it2.403
r_angle_refined_deg1.729
r_scbond_it1.575
r_mcangle_it1.021
r_mcbond_it0.611
r_nbtor_refined0.302
r_symmetry_hbond_refined0.224
r_nbd_refined0.204
r_metal_ion_refined0.201
r_xyhbond_nbd_refined0.19
r_symmetry_vdw_refined0.145
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12417
Nucleic Acid Atoms
Solvent Atoms832
Heterogen Atoms438

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction