X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 10% PEG 8000, 5% iso-propanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.64 α = 90
b = 68.22 β = 91.48
c = 94.02 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 MAR scanner 300 mm plate -- 2011-06-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID -- APS 22-ID

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
2.1 50 88.4 0.058 0.076 -- 3.3 49234 43523 0.0 0.0 34.5
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)
2.1 2.14 46.8 0.447 0.076 1.49 3.3 --

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 2.1 25.067 -- 1.42 49376 41640 2070 84.41 -- 0.1947 0.1927 0.2319 --
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 2.0798 2.1282 -- 35 1222 0.2707 0.2968 -- 38.0
X Ray Diffraction 2.1282 2.1813 -- 72 1651 0.265 0.3154 -- 53.0
X Ray Diffraction 2.1813 2.2403 -- 94 2043 0.2508 0.3027 -- 65.0
X Ray Diffraction 2.2403 2.3062 -- 133 2303 0.2434 0.3038 -- 75.0
X Ray Diffraction 2.3062 2.3805 -- 141 2525 0.2268 0.3058 -- 83.0
X Ray Diffraction 2.3805 2.4656 -- 147 2703 0.2307 0.2801 -- 86.0
X Ray Diffraction 2.4656 2.5642 -- 166 2843 0.2214 0.2676 -- 92.0
X Ray Diffraction 2.5642 2.6808 -- 169 2907 0.21 0.2506 -- 94.0
X Ray Diffraction 2.6808 2.8219 -- 137 2993 0.215 0.2483 -- 95.0
X Ray Diffraction 2.8219 2.9984 -- 177 2974 0.2131 0.2526 -- 97.0
X Ray Diffraction 2.9984 3.2295 -- 158 3042 0.2032 0.2615 -- 97.0
X Ray Diffraction 3.2295 3.5537 -- 147 3036 0.1975 0.2256 -- 97.0
X Ray Diffraction 3.5537 4.066 -- 174 3062 0.1757 0.2138 -- 97.0
X Ray Diffraction 4.066 5.1156 -- 161 3061 0.1597 0.1969 -- 98.0
X Ray Diffraction 5.1156 25.0687 -- 159 3205 0.1754 0.2025 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.4595
Anisotropic B[1][1] 6.3432
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -5.0073
Anisotropic B[2][2] 2.1836
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.5268
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.01
f_chiral_restr 0.033
f_dihedral_angle_d 11.647
f_angle_d 0.526
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5308
Nucleic Acid Atoms 0
Heterogen Atoms 384
Solvent Atoms 241

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement