X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 300.0
Details 50 mM Sodium Cacodylate, 50-125 Sodium Citrate, 10-20 % isopropanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.54 α = 90
b = 133.57 β = 90
c = 230.27 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Varimax-HF 2009-04-10
Diffraction Radiation
Monochromator Protocol
Varimax-HF SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5416 -- --

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
2.73 50 94.9 0.097 -- -- 5.6 -- 55922 -- -- --
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)
2.734 2.85 95.9 0.502 -- -- 5.3 --

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 2.734 33.819 -- 1.34 -- 55770 2852 94.11 -- 0.222 0.2194 0.2699 --
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 2.734 2.7814 -- 110 2227 0.2632 0.3468 -- 80.0
X Ray Diffraction 2.7814 2.8319 -- 136 2659 0.2582 0.3074 -- 96.0
X Ray Diffraction 2.8319 2.8864 -- 142 2639 0.2485 0.326 -- 95.0
X Ray Diffraction 2.8864 2.9452 -- 146 2644 0.2405 0.344 -- 96.0
X Ray Diffraction 2.9452 3.0092 -- 162 2621 0.2344 0.2849 -- 95.0
X Ray Diffraction 3.0092 3.0792 -- 134 2634 0.218 0.3235 -- 95.0
X Ray Diffraction 3.0792 3.1562 -- 140 2641 0.2193 0.2812 -- 94.0
X Ray Diffraction 3.1562 3.2414 -- 149 2616 0.2267 0.3251 -- 94.0
X Ray Diffraction 3.2414 3.3367 -- 144 2579 0.2247 0.3142 -- 93.0
X Ray Diffraction 3.3367 3.4443 -- 138 2606 0.2167 0.2683 -- 93.0
X Ray Diffraction 3.4443 3.5673 -- 156 2573 0.2123 0.2579 -- 93.0
X Ray Diffraction 3.5673 3.71 -- 140 2548 0.212 0.2729 -- 91.0
X Ray Diffraction 3.71 3.8786 -- 114 2567 0.2176 0.2835 -- 91.0
X Ray Diffraction 3.8786 4.0827 -- 130 2545 0.2048 0.2419 -- 90.0
X Ray Diffraction 4.0827 4.338 -- 139 2588 0.1766 0.2245 -- 92.0
X Ray Diffraction 4.338 4.6722 -- 154 2671 0.1588 0.2087 -- 95.0
X Ray Diffraction 4.6722 5.1409 -- 139 2847 0.1735 0.1962 -- 99.0
X Ray Diffraction 5.1409 5.8814 -- 155 2841 0.1959 0.2595 -- 100.0
X Ray Diffraction 5.8814 7.3972 -- 167 2875 0.2325 0.2672 -- 100.0
X Ray Diffraction 7.3972 33.822 -- 157 2997 0.2459 0.2687 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 56.528
Anisotropic B[1][1] 1.626
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.757
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.131
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.044
f_angle_d 0.793
f_bond_d 0.004
f_plane_restr 0.004
f_dihedral_angle_d 14.092
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13375
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 208

Software

Software
Software Name Purpose
HKL data processing
PHASER phasing
PHENIX refinement version: 1.5_2
PDB_EXTRACT data extraction version: 3.005
StructureStudio data collection
HKL data reduction
HKL data scaling