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
3.0459.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.665α = 90
b = 82.745β = 100.4
c = 125.791γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0000ALS8.2.2

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
12.55099.60.07515.54.26184522
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)
2.52.5998.30.4054.2

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 2P1M2.55061845330290.510.198630.194580.27405RANDOM7.709
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]
0.821.491.19-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.506
r_dihedral_angle_4_deg24.877
r_dihedral_angle_3_deg24.518
r_dihedral_angle_1_deg12.245
r_scangle_it11.919
r_scbond_it11.017
r_mcangle_it5.968
r_mcbond_it5.213
r_angle_refined_deg2.793
r_chiral_restr0.719
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.506
r_dihedral_angle_4_deg24.877
r_dihedral_angle_3_deg24.518
r_dihedral_angle_1_deg12.245
r_scangle_it11.919
r_scbond_it11.017
r_mcangle_it5.968
r_mcbond_it5.213
r_angle_refined_deg2.793
r_chiral_restr0.719
r_nbtor_refined0.359
r_nbd_refined0.309
r_symmetry_vdw_refined0.305
r_xyhbond_nbd_refined0.219
r_symmetry_hbond_refined0.189
r_bond_refined_d0.029
r_gen_planes_refined0.01
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 Atoms11250
Nucleic Acid Atoms
Solvent Atoms524
Heterogen Atoms98

Software

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