X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details 1.2 M NaH2PO4/0.8 M K2HPO4, 0.2 M Li2SO4, 0.1 M CAPS (pH 10.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.75 α = 78.16
b = 47.28 β = 62.99
c = 47.37 γ = 63.14
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 300 mm plate MIRRORS 2010-02-25
Diffraction Radiation
Monochromator Protocol
ROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM- ROCK VERTICAL FOCUSING MIRROR MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.9795, 0.9793, 0.9718 APS 22-BM

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
1.1 22.64 92.0 0.079 -- -- 3.81 -- 86175 1.0 3.0 --
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)
1.1 1.14 83.1 0.434 -- 2.1 3.73 9892

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
MAD 1.2 22.64 -- 1.0 77522 77522 8658 93.46 -- -- 0.14024 0.16923 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 1.2 1.231 -- 600 5528 0.21 0.255 -- 90.96
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 13.854
Anisotropic B[1][1] 2.76
Anisotropic B[1][2] 0.19
Anisotropic B[1][3] -1.34
Anisotropic B[2][2] -1.23
Anisotropic B[2][3] 0.5
Anisotropic B[3][3] -0.69
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.746
r_dihedral_angle_1_deg 6.111
r_scbond_it 6.83
r_angle_refined_deg 1.356
r_sphericity_bonded 13.59
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_mcangle_it 4.926
r_chiral_restr 0.099
r_dihedral_angle_3_deg 11.352
r_bond_refined_d 0.013
r_bond_other_d 0.0
r_rigid_bond_restr 4.157
r_dihedral_angle_2_deg 43.628
r_mcbond_it 3.777
r_mcbond_other 2.525
r_dihedral_angle_4_deg 7.403
r_scangle_it 8.27
r_sphericity_free 25.579
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1966
Nucleic Acid Atoms 0
Heterogen Atoms 56
Solvent Atoms 344

Software

Software
Software Name Purpose
d*TREK data scaling
PHENIX model building
PHASER phasing
REFMAC refinement version: 5.5.0044
d*TREK data reduction
PHENIX phasing