X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 0.9 M sodium malonate pH 7.0, 0.1 M HEPES pH 7.0, 5% (v/v) glycerol, 56 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 84.7 α = 90
b = 106.62 β = 90
c = 154.22 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
CCD MARMOSAIC 300 mm CCD Vertical focusing mirrors 2012-05-16
Diffraction Radiation
Monochromator Protocol
ACCEL/BRUKER DCM, Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 1.2824 CLSI 08ID-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
2.8 53.33 99.9 0.079 -- -- 9.7 35155 35121 1.0 1.0 --
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)
2.8 2.95 100.0 0.464 0.464 1.6 9.7 5044

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
SAD 2.8 53.31 -- 1.36 35131 35065 1782 99.81 0.187 0.1869 0.1844 0.233 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 2.7994 2.8751 2488 133 2488 0.2863 0.3181 -- 100.0
X Ray Diffraction 2.8751 2.9597 2554 133 2554 0.242 0.2901 -- 100.0
X Ray Diffraction 2.9597 3.0552 2512 135 2512 0.2276 0.3029 -- 100.0
X Ray Diffraction 3.0552 3.1644 2548 125 2548 0.2256 0.2834 -- 100.0
X Ray Diffraction 3.1644 3.291 2542 141 2542 0.2193 0.3035 -- 100.0
X Ray Diffraction 3.291 3.4408 2525 134 2525 0.2129 0.2959 -- 100.0
X Ray Diffraction 3.4408 3.6222 2524 145 2524 0.1875 0.2311 -- 100.0
X Ray Diffraction 3.6222 3.8491 2574 131 2574 0.1792 0.2299 -- 100.0
X Ray Diffraction 3.8491 4.1461 2545 135 2545 0.1636 0.208 -- 100.0
X Ray Diffraction 4.1461 4.5632 2578 141 2578 0.1505 0.1731 -- 100.0
X Ray Diffraction 4.5632 5.223 2584 146 2584 0.1517 0.1965 -- 100.0
X Ray Diffraction 5.223 6.5785 2599 143 2599 0.1721 0.2272 -- 100.0
X Ray Diffraction 6.5785 53.3221 2710 140 2710 0.1817 0.2209 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.4322
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.914
f_chiral_restr 0.066
f_bond_d 0.01
f_dihedral_angle_d 14.677
f_plane_restr 0.004
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.337
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7195
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 45

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.20
SOLVE phasing
RESOLVE phasing
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.11
MxDC data collection
PHENIX phasing version: 1.8.2_1309