X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DSR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82931.3 M sodium citrate, 50 mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.0840.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.132α = 90
b = 41.302β = 104.267
c = 72.209γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702019-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)0.9793PAL/PLS7A (6B, 6C1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.23095.50.0580.0620.0230.99928.87.572028
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2292.60.3680.3960.1450.9516.87.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5DSR1.23072011368895.4670.1110.10990.137513.342
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]
0.178-0.115-0.1430.02
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free46.904
r_dihedral_angle_2_deg35.171
r_dihedral_angle_4_deg25.736
r_sphericity_bonded13.973
r_dihedral_angle_3_deg11.553
r_dihedral_angle_1_deg6.922
r_rigid_bond_restr6.421
r_lrange_it6.04
r_lrange_other5.444
r_scangle_it4.073
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free46.904
r_dihedral_angle_2_deg35.171
r_dihedral_angle_4_deg25.736
r_sphericity_bonded13.973
r_dihedral_angle_3_deg11.553
r_dihedral_angle_1_deg6.922
r_rigid_bond_restr6.421
r_lrange_it6.04
r_lrange_other5.444
r_scangle_it4.073
r_scangle_other4.072
r_scbond_it3.729
r_scbond_other3.729
r_mcangle_other2.589
r_mcangle_it2.579
r_angle_refined_deg2.515
r_mcbond_it2.05
r_mcbond_other2.029
r_angle_other_deg1.288
r_symmetry_nbd_refined0.326
r_nbd_refined0.292
r_nbd_other0.286
r_symmetry_xyhbond_nbd_refined0.215
r_chiral_restr0.213
r_nbtor_refined0.188
r_symmetry_nbd_other0.181
r_xyhbond_nbd_refined0.138
r_symmetry_nbtor_other0.089
r_symmetry_xyhbond_nbd_other0.033
r_bond_refined_d0.031
r_gen_planes_refined0.014
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing