X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2P1MPDB ENTRY: 2P1M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298100 mM BTP, 10% 14% PEG 20,000, 200 mM NaCl, and 5 mM DTT, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9358.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.207α = 90
b = 82.472β = 104.05
c = 125.053γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0000ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.915099.90.039333.86979369793
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.912.031000.2494.93.6

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: 2P1M1.915069793373394.440.173860.171770.21333RANDOM27.399
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]
0.530.371.12-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.843
r_dihedral_angle_4_deg18.329
r_dihedral_angle_3_deg15.518
r_dihedral_angle_1_deg5.826
r_scangle_it3.608
r_scbond_it2.373
r_angle_refined_deg1.634
r_mcangle_it1.258
r_mcbond_it0.862
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.843
r_dihedral_angle_4_deg18.329
r_dihedral_angle_3_deg15.518
r_dihedral_angle_1_deg5.826
r_scangle_it3.608
r_scbond_it2.373
r_angle_refined_deg1.634
r_mcangle_it1.258
r_mcbond_it0.862
r_nbtor_refined0.312
r_symmetry_vdw_refined0.219
r_nbd_refined0.211
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.163
r_chiral_restr0.137
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5582
Nucleic Acid Atoms
Solvent Atoms770
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing