X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 298.0
Details 15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.23 α = 90
b = 78.29 β = 90
c = 94.09 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-07-02
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.5 50 88.1 0.067 -- -- 3.6 -- 80130 1.0 1.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.5 1.55 96.3 0.447 -- -- 2.8 8619

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.5 34.27 -- 0.0 -- 80075 4216 88.01 -- 0.1661 0.1639 0.2049 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.5 1.537 -- 335 5890 0.159 0.251 -- 93.51
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.4173
Anisotropic B[1][1] -0.59
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.18
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.214
r_mcbond_it 2.466
r_rigid_bond_restr 2.045
r_sphericity_free 11.068
r_chiral_restr 0.118
r_sphericity_bonded 4.693
r_dihedral_angle_3_deg 13.447
r_nbtor_other 0.086
r_symmetry_hbond_refined 0.16
r_angle_refined_deg 1.814
r_mcangle_it 2.915
r_mcbond_other 0.93
r_scbond_it 4.084
r_scangle_it 5.308
r_bond_refined_d 0.022
r_gen_planes_refined 0.009
r_bond_other_d 0.001
r_nbd_refined 0.235
r_nbtor_refined 0.182
r_symmetry_vdw_other 0.248
r_angle_other_deg 0.885
r_nbd_other 0.186
r_dihedral_angle_2_deg 40.098
r_dihedral_angle_4_deg 16.987
r_gen_planes_other 0.002
r_metal_ion_refined 0.091
r_symmetry_vdw_refined 0.209
r_dihedral_angle_1_deg 5.866
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3575
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 518

Software

Software
Software Name Purpose
SCALEPACK data scaling
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.11
CLS data collection
DENZO data reduction
REFMAC phasing version: 5.2.0005