X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O4BPDB ENTRY 4O4B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Micro Seeding5.22988% (w/v) PEG 3350, 100 mM Na3Citrate, pH 5.2 at 25C, Micro Seeding, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2344.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.418α = 90
b = 128.371β = 114.26
c = 52.526γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
11.95098.60.078253.7251513
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)
11.91.9393.30.2353.631927

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4O4B2.232.112515125151133599.220.231780.231780.228960.28561RANDOM25.328
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]
-0.32-0.071.14-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.642
r_dihedral_angle_3_deg15.581
r_dihedral_angle_4_deg14.024
r_dihedral_angle_1_deg5.832
r_long_range_B_refined5.464
r_long_range_B_other5.278
r_mcangle_it2.119
r_mcangle_other2.119
r_scangle_other1.577
r_mcbond_it1.184
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.642
r_dihedral_angle_3_deg15.581
r_dihedral_angle_4_deg14.024
r_dihedral_angle_1_deg5.832
r_long_range_B_refined5.464
r_long_range_B_other5.278
r_mcangle_it2.119
r_mcangle_other2.119
r_scangle_other1.577
r_mcbond_it1.184
r_mcbond_other1.183
r_angle_refined_deg1.181
r_scbond_it0.885
r_scbond_other0.885
r_angle_other_deg0.833
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4020
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing