X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z2U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29722% PEG3350, 0.19M Ca(AC)2, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
1.9837.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.004α = 90
b = 58.004β = 90
c = 117.114γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVVeriMax HR2006-01-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.54

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
11.863099.90.0640.06410.114.4104461044631.8
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)
1.861.8999.80.9780.9782.3813.8495

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 REPLACEMENTTHROUGHOUT1Z2U1.863010446963978099.910.208630.208630.204380.26251RANDOM31.603
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]
0.630.320.63-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.592
r_dihedral_angle_3_deg12.407
r_dihedral_angle_4_deg8.091
r_dihedral_angle_1_deg4.633
r_scangle_it3.831
r_mcangle_it3.546
r_scbond_it2.813
r_mcbond_it2.551
r_angle_refined_deg1.454
r_symmetry_vdw_refined0.355
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.592
r_dihedral_angle_3_deg12.407
r_dihedral_angle_4_deg8.091
r_dihedral_angle_1_deg4.633
r_scangle_it3.831
r_mcangle_it3.546
r_scbond_it2.813
r_mcbond_it2.551
r_angle_refined_deg1.454
r_symmetry_vdw_refined0.355
r_nbtor_refined0.307
r_nbd_refined0.196
r_symmetry_hbond_refined0.154
r_xyhbond_nbd_refined0.123
r_chiral_restr0.077
r_bond_refined_d0.017
r_gen_planes_refined0.005
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 Atoms882
Nucleic Acid Atoms
Solvent Atoms101
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
PHASERphasing
Cootmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building