X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details 0.1 M BIS-TRIS PROPANE PH 6.5, 0.3-0.9 M SODIUM POTASSIUM TARTRATE, 0.0006 M PROTEIN, 0.0014 M LANTHANIDE COMPLEX, 293 K, 5 DAYS

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.85 α = 90
b = 57.85 β = 90
c = 150.21 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 MIRRORS 2010-11-27
Diffraction Radiation
Monochromator Protocol
EITHER 111 OR 311 SILICON SINGLE CRISTALS MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM30A -- ESRF BM30A

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
1.2 45.83 98.0 0.05 -- -- 9.9 -- 78373 -- 3.0 9.4
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)
1.2 1.26 95.8 0.46 -- 1.7 10.0 --

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
MAD 1.2 31.499 -- 1.35 -- 78332 3920 97.14 -- 0.1379 0.1369 0.1553 --
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 1.1999 1.2145 -- 134 2537 0.1708 0.2108 -- 94.0
X Ray Diffraction 1.2145 1.2299 -- 133 2575 0.16 0.1929 -- 95.0
X Ray Diffraction 1.2299 1.2461 -- 131 2538 0.1495 0.1798 -- 95.0
X Ray Diffraction 1.2461 1.2631 -- 135 2585 0.1411 0.1352 -- 95.0
X Ray Diffraction 1.2631 1.2812 -- 135 2575 0.1339 0.1798 -- 96.0
X Ray Diffraction 1.2812 1.3003 -- 134 2567 0.1321 0.164 -- 96.0
X Ray Diffraction 1.3003 1.3206 -- 136 2611 0.1322 0.1946 -- 96.0
X Ray Diffraction 1.3206 1.3423 -- 137 2582 0.1263 0.154 -- 96.0
X Ray Diffraction 1.3423 1.3654 -- 139 2590 0.1156 0.1495 -- 96.0
X Ray Diffraction 1.3654 1.3903 -- 138 2612 0.1141 0.1632 -- 96.0
X Ray Diffraction 1.3903 1.417 -- 138 2612 0.1128 0.1474 -- 97.0
X Ray Diffraction 1.417 1.4459 -- 137 2609 0.1077 0.1295 -- 97.0
X Ray Diffraction 1.4459 1.4774 -- 137 2622 0.1036 0.168 -- 97.0
X Ray Diffraction 1.4774 1.5117 -- 140 2634 0.1035 0.1412 -- 97.0
X Ray Diffraction 1.5117 1.5495 -- 140 2639 0.0941 0.1331 -- 97.0
X Ray Diffraction 1.5495 1.5914 -- 141 2643 0.0949 0.1293 -- 97.0
X Ray Diffraction 1.5914 1.6383 -- 143 2656 0.097 0.1203 -- 97.0
X Ray Diffraction 1.6383 1.6911 -- 141 2661 0.0985 0.1354 -- 98.0
X Ray Diffraction 1.6911 1.7516 -- 138 2679 0.106 0.1333 -- 98.0
X Ray Diffraction 1.7516 1.8217 -- 141 2688 0.1136 0.1398 -- 98.0
X Ray Diffraction 1.8217 1.9046 -- 143 2680 0.1203 0.142 -- 98.0
X Ray Diffraction 1.9046 2.005 -- 145 2701 0.119 0.1569 -- 98.0
X Ray Diffraction 2.005 2.1306 -- 142 2726 0.1302 0.1354 -- 99.0
X Ray Diffraction 2.1306 2.295 -- 145 2729 0.1316 0.1641 -- 99.0
X Ray Diffraction 2.295 2.5259 -- 147 2763 0.1469 0.1559 -- 99.0
X Ray Diffraction 2.5259 2.8912 -- 147 2784 0.1602 0.1766 -- 99.0
X Ray Diffraction 2.8912 3.6418 -- 149 2841 0.1568 0.1646 -- 100.0
X Ray Diffraction 3.6418 31.51 -- 154 2973 0.1821 0.1609 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.77
Anisotropic B[1][1] 0.8311
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.8311
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.6621
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.014
f_chiral_restr 0.099
f_angle_d 1.612
f_dihedral_angle_d 19.032
f_plane_restr 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1551
Nucleic Acid Atoms 0
Heterogen Atoms 61
Solvent Atoms 411

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
SCALA data scaling version: 3.3.16
SHARP phasing