X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 292.0
Details 16-18% PEG 3350, 250 mM NaCl and 100 mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.84 α = 90
b = 181.35 β = 90
c = 196.57 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 mirror 2010-03-04
Diffraction Radiation
Monochromator Protocol
Diamond crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1

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
2.45 48.86 96.3 0.113 0.419 -- 5.8 95492 91957 0.0 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)
2.45 2.58 88.6 0.348 0.419 4.3 4.9 --

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
using phases from it's GanBE323A mutant 2.448 48.859 -- 1.35 91878 91872 4594 96.23 -- 0.1365 0.1329 0.2045 --
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 2.448 2.4758 -- 146 2605 0.1572 0.2691 -- 87.0
X Ray Diffraction 2.4758 2.5049 -- 125 2642 0.1672 0.2635 -- 89.0
X Ray Diffraction 2.5049 2.5355 -- 131 2614 0.1655 0.2714 -- 87.0
X Ray Diffraction 2.5355 2.5676 -- 143 2650 0.1589 0.2645 -- 88.0
X Ray Diffraction 2.5676 2.6014 -- 151 2659 0.1549 0.2628 -- 90.0
X Ray Diffraction 2.6014 2.637 -- 153 2690 0.1499 0.2291 -- 90.0
X Ray Diffraction 2.637 2.6747 -- 152 2698 0.1466 0.2492 -- 90.0
X Ray Diffraction 2.6747 2.7146 -- 152 2757 0.146 0.2355 -- 93.0
X Ray Diffraction 2.7146 2.757 -- 144 2795 0.1435 0.2215 -- 93.0
X Ray Diffraction 2.757 2.8022 -- 134 2811 0.1432 0.2455 -- 95.0
X Ray Diffraction 2.8022 2.8505 -- 159 2879 0.1427 0.2458 -- 96.0
X Ray Diffraction 2.8505 2.9023 -- 168 2843 0.1456 0.2497 -- 96.0
X Ray Diffraction 2.9023 2.9582 -- 152 2915 0.1468 0.2216 -- 97.0
X Ray Diffraction 2.9582 3.0185 -- 144 2947 0.1451 0.2186 -- 98.0
X Ray Diffraction 3.0185 3.0842 -- 154 2974 0.1389 0.2095 -- 99.0
X Ray Diffraction 3.0842 3.1559 -- 157 2974 0.1363 0.2286 -- 99.0
X Ray Diffraction 3.1559 3.2348 -- 163 2991 0.1348 0.2161 -- 100.0
X Ray Diffraction 3.2348 3.3222 -- 166 2979 0.1259 0.2077 -- 100.0
X Ray Diffraction 3.3222 3.42 -- 151 3062 0.1245 0.1919 -- 100.0
X Ray Diffraction 3.42 3.5303 -- 188 2957 0.1185 0.1907 -- 100.0
X Ray Diffraction 3.5303 3.6565 -- 155 3011 0.119 0.169 -- 100.0
X Ray Diffraction 3.6565 3.8028 -- 143 3067 0.1207 0.2076 -- 100.0
X Ray Diffraction 3.8028 3.9758 -- 159 3020 0.1169 0.1542 -- 100.0
X Ray Diffraction 3.9758 4.1853 -- 140 3068 0.1101 0.1545 -- 100.0
X Ray Diffraction 4.1853 4.4474 -- 142 3046 0.1064 0.1744 -- 100.0
X Ray Diffraction 4.4474 4.7905 -- 176 3065 0.108 0.1516 -- 100.0
X Ray Diffraction 4.7905 5.2721 -- 149 3056 0.1168 0.1814 -- 100.0
X Ray Diffraction 5.2721 6.0338 -- 163 3105 0.1405 0.1889 -- 100.0
X Ray Diffraction 6.0338 7.5973 -- 168 3118 0.1525 0.2037 -- 100.0
X Ray Diffraction 7.5973 48.8683 -- 166 3280 0.1485 0.17 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 13.375
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.15
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.426
f_angle_d 1.09
f_chiral_restr 0.041
f_bond_d 0.008
f_plane_restr 0.004
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.2369
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 16922
Nucleic Acid Atoms 0
Heterogen Atoms 153
Solvent Atoms 1504

Software

Software
Software Name Purpose
ADSC data collection version: Quantum
REFMAC refinement
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
MOSFLM data reduction
SCALA data scaling
REFMAC phasing