X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 0.2 M sodium nitrate and 20% (w/v) polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.27 α = 90
b = 67.09 β = 101.3
c = 87.67 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
IMAGE PLATE RIGAKU RAXIS VII -- 2010-11-13
Diffraction Radiation
Monochromator Protocol
Si 111 channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.5418 -- --

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
2.4 50 99.9 0.18 0.18 -- 4.1 33037 33004 3.0 0.0 --
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)
2.4 2.49 99.8 0.483 0.483 2.38 3.8 3267

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 2.4 40.671 -- 0.15 -- 31150 1581 93.94 -- 0.2417 0.2392 0.289 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 2.4035 2.481 -- 146 2304 0.274 0.3306 -- 83.0
X Ray Diffraction 2.481 2.5697 -- 140 2544 0.2728 0.368 -- 89.0
X Ray Diffraction 2.5697 2.6726 -- 122 2578 0.27 0.3385 -- 90.0
X Ray Diffraction 2.6726 2.7942 -- 137 2624 0.2667 0.3469 -- 92.0
X Ray Diffraction 2.7942 2.9415 -- 132 2653 0.2602 0.3158 -- 93.0
X Ray Diffraction 2.9415 3.1257 -- 145 2720 0.259 0.2953 -- 95.0
X Ray Diffraction 3.1257 3.3669 -- 145 2770 0.2384 0.298 -- 97.0
X Ray Diffraction 3.3669 3.7055 -- 143 2832 0.2196 0.2769 -- 98.0
X Ray Diffraction 3.7055 4.2413 -- 149 2807 0.2026 0.248 -- 98.0
X Ray Diffraction 4.2413 5.3416 -- 142 2852 0.1868 0.2327 -- 99.0
X Ray Diffraction 5.3416 40.6764 -- 180 2885 0.2411 0.2542 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 5.5793
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.6486
Anisotropic B[2][2] -1.8467
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.7326
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.05
f_dihedral_angle_d 18.366
f_angle_d 0.708
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6262
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 402

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
AMoRE Structure Solution
PHENIX (phenix.refine: 1.5_2) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.5_2) refinement
AMoRE model building
CrystalClear data collection