X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 290.0
Details microseeding in 100 mM Tris pH=9.0, 10% PEG 3350 (w/v), 8% 2-propanol (v/v), 0.12 M phenol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.43 α = 90
b = 107.65 β = 106.69
c = 68.72 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
2.25 50 97.6 0.047 -- -- 2.7 42106 41096 -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)
2.25 2.29 92.6 0.359 -- -- 2.5 1945

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
SAD 2.25 47.438 -- 1.35 41069 41069 1295 97.44 -- 0.208 0.207 0.254 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 2.247 2.336 -- 124 4233 0.292 0.354 -- 94.0
X Ray Diffraction 2.336 2.443 -- 136 4476 0.271 0.342 -- 99.0
X Ray Diffraction 2.443 2.572 -- 142 4469 0.243 0.308 -- 99.0
X Ray Diffraction 2.572 2.733 -- 152 4495 0.237 0.295 -- 99.0
X Ray Diffraction 2.733 2.944 -- 167 4430 0.226 0.318 -- 99.0
X Ray Diffraction 2.944 3.24 -- 134 4486 0.224 0.275 -- 99.0
X Ray Diffraction 3.24 3.708 -- 144 4442 0.204 0.24 -- 98.0
X Ray Diffraction 3.708 4.672 -- 150 4401 0.175 0.213 -- 97.0
X Ray Diffraction 4.672 47.449 -- 146 4342 0.19 0.231 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.952
Anisotropic B[1][1] -0.76
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.883
Anisotropic B[2][2] -2.289
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.049
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.762
f_plane_restr 0.003
f_chiral_restr 0.042
f_angle_d 0.674
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6436
Nucleic Acid Atoms 298
Heterogen Atoms 14
Solvent Atoms 136

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
SHARP Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.006 data extraction
phenix refinement
Solomon density modification
SHARP phasing
HKL data processing