X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 294.0
Details 0.1 M MES (pH 6.5), 20% (w/v) PEG 8K and 2.4% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.32 α = 90
b = 112.3 β = 99.55
c = 61.11 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
2 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-02-17
CCD MARMOSAIC 225 mm CCD -- 2009-02-16
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.97872 APS 21-ID-D
SYNCHROTRON APS BEAMLINE 22-BM 0.9792 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
2.28 29.1 99.6 -- 0.109 -- 4.8 32231 32231 -3.0 -3.0 40.8
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)
2.28 2.38 98.1 -- 0.404 2.5 3.4 3176

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 2.28 29.1 -- 1.35 32199 32188 1631 97.29 0.2362 0.1869 0.1849 0.2254 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 2.277 2.3439 -- 86 1871 0.2176 0.2383 -- 71.0
X Ray Diffraction 2.3439 2.4196 -- 148 2544 0.2039 0.2625 -- 99.0
X Ray Diffraction 2.4196 2.506 -- 147 2601 0.1979 0.2754 -- 100.0
X Ray Diffraction 2.506 2.6063 -- 141 2602 0.206 0.2346 -- 100.0
X Ray Diffraction 2.6063 2.7248 -- 145 2604 0.2084 0.2623 -- 100.0
X Ray Diffraction 2.7248 2.8683 -- 148 2610 0.2102 0.2456 -- 100.0
X Ray Diffraction 2.8683 3.0479 -- 136 2616 0.1981 0.2699 -- 100.0
X Ray Diffraction 3.0479 3.2829 -- 127 2625 0.1911 0.2085 -- 100.0
X Ray Diffraction 3.2829 3.6127 -- 131 2623 0.1671 0.2429 -- 100.0
X Ray Diffraction 3.6127 4.1342 -- 139 2626 0.1537 0.1824 -- 100.0
X Ray Diffraction 4.1342 5.2038 -- 132 2628 0.146 0.1764 -- 100.0
X Ray Diffraction 5.2038 29.1056 -- 151 2607 0.1681 0.2009 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -7.1752
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.0957
Anisotropic B[2][2] -2.3552
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.5304
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.068
f_dihedral_angle_d 21.87
f_angle_d 1.185
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3184
Nucleic Acid Atoms 845
Heterogen Atoms 2
Solvent Atoms 112

Software

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