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_sphericity_bonded 4.693
r_sphericity_free 11.068
r_rigid_bond_restr 2.045
r_scangle_it 5.308
r_nbd_refined 0.235
r_gen_planes_other 0.002
r_gen_planes_refined 0.009
r_chiral_restr 0.118
r_dihedral_angle_4_deg 16.987
r_dihedral_angle_3_deg 13.447
r_dihedral_angle_2_deg 40.098
r_dihedral_angle_1_deg 5.866
r_angle_other_deg 0.885
r_angle_refined_deg 1.814
r_bond_other_d 0.001
r_bond_refined_d 0.022
r_nbd_other 0.186
r_nbtor_refined 0.182
r_nbtor_other 0.086
r_xyhbond_nbd_refined 0.214
r_metal_ion_refined 0.091
r_symmetry_vdw_refined 0.209
r_symmetry_vdw_other 0.248
r_symmetry_hbond_refined 0.16
r_mcbond_it 2.466
r_mcbond_other 0.93
r_mcangle_it 2.915
r_scbond_it 4.084
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

Computing
Computing Package Purpose
CLS Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.2.0005 Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.2.0005 refinement
SCALEPACK data reduction