X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 291.0
Details 50mM Imidazole, 350mM Sodium Acetate, 16.5% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.03 α = 90
b = 79.45 β = 96.96
c = 102.09 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 RIGAKU SATURN 92 mirrors 2011-06-21
Diffraction Radiation
Monochromator Protocol
mirrors VarimaxHF SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178 -- --

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
2.2 50 99.7 0.136 -- -- 5.9 263254 263254 0.0 -3.0 31.2
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)
2.2 2.28 100.0 0.703 -- 2.73 5.8 --

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 2.2 21.36 -- 0.0 74621 74621 1393 85.78 0.2122 0.2122 0.2097 0.2776 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 2.2 2.24 -- 145 3615 0.2626 0.3502 -- 83.0
X Ray Diffraction 2.24 2.283 -- 144 3371 0.2572 0.3312 -- 77.0
X Ray Diffraction 2.283 2.3296 -- 142 3562 0.2494 0.3378 -- 81.0
X Ray Diffraction 2.3296 2.3801 -- 150 3677 0.2395 0.3133 -- 82.0
X Ray Diffraction 2.3801 2.4354 -- 128 3385 0.2558 0.2795 -- 77.0
X Ray Diffraction 2.4354 2.4962 -- 124 3452 0.2546 0.3663 -- 78.0
X Ray Diffraction 2.4962 2.5636 -- 122 3353 0.2774 0.4073 -- 77.0
X Ray Diffraction 2.5636 2.6389 -- 133 3425 0.2616 0.3453 -- 78.0
X Ray Diffraction 2.6389 2.724 -- 131 3486 0.2578 0.3461 -- 79.0
X Ray Diffraction 2.724 2.8211 -- 122 3467 0.251 0.3311 -- 77.0
X Ray Diffraction 2.8211 2.9338 -- 123 3484 0.2422 0.2968 -- 79.0
X Ray Diffraction 2.9338 3.0669 -- 140 3624 0.23 0.3261 -- 83.0
X Ray Diffraction 3.0669 3.2281 -- 150 4189 0.2276 0.3185 -- 94.0
X Ray Diffraction 3.2281 3.4296 -- 161 4302 0.2152 0.3107 -- 98.0
X Ray Diffraction 3.4296 3.6931 -- 167 4422 0.2143 0.2872 -- 99.0
X Ray Diffraction 3.6931 4.0625 -- 158 4200 0.1709 0.219 -- 96.0
X Ray Diffraction 4.0625 4.6451 -- 158 4222 0.1474 0.2134 -- 95.0
X Ray Diffraction 4.6451 5.8325 -- 159 4255 0.1756 0.208 -- 97.0
X Ray Diffraction 5.8325 21.3611 -- 167 4406 0.1957 0.2319 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -5.8979
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.2014
Anisotropic B[2][2] -0.3574
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.2553
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.062
f_dihedral_angle_d 21.512
f_angle_d 1.1
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5152
Nucleic Acid Atoms 1264
Heterogen Atoms 68
Solvent Atoms 414

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
CNS model building
StructureStudio data collection