X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch Crystallization Under Oil
pH 5
Temperature 277.0
Details 40 % PEG 400, 0.1 M Ammonium phosphate monobasic, 0.1 M Sodium acetate, pH 5.0, Microbatch crystallization under oil, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.96 α = 90
b = 60.96 β = 90
c = 118.66 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2011-06-09
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.97915 NSLS X4C

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
1.5 50 98.4 0.073 -- -- 7.2 41749 41081 0.0 0.0 14.18
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)
1.5 1.55 92.5 0.491 -- 3.2 4.0 4119

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 1.5 39.44 -- 1.34 -- 41049 2075 98.46 -- 0.16 0.158 0.193 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 1.5 1.535 -- 135 2383 0.233 0.298 -- 91.0
X Ray Diffraction 1.535 1.573 -- 137 2443 0.201 0.251 -- 94.0
X Ray Diffraction 1.573 1.616 -- 146 2487 0.169 0.236 -- 97.0
X Ray Diffraction 1.616 1.663 -- 123 2574 0.157 0.234 -- 98.0
X Ray Diffraction 1.663 1.717 -- 159 2544 0.136 0.189 -- 99.0
X Ray Diffraction 1.717 1.778 -- 137 2598 0.132 0.176 -- 99.0
X Ray Diffraction 1.778 1.85 -- 131 2652 0.128 0.197 -- 100.0
X Ray Diffraction 1.85 1.934 -- 132 2578 0.121 0.169 -- 100.0
X Ray Diffraction 1.934 2.036 -- 131 2663 0.13 0.165 -- 100.0
X Ray Diffraction 2.036 2.163 -- 153 2579 0.132 0.175 -- 100.0
X Ray Diffraction 2.163 2.33 -- 143 2648 0.145 0.175 -- 100.0
X Ray Diffraction 2.33 2.565 -- 138 2650 0.153 0.21 -- 100.0
X Ray Diffraction 2.565 2.936 -- 130 2683 0.171 0.163 -- 100.0
X Ray Diffraction 2.936 3.698 -- 127 2702 0.173 0.191 -- 100.0
X Ray Diffraction 3.698 39.454 -- 153 2790 0.176 0.203 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.707
Anisotropic B[1][1] 0.627
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.627
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.254
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.006
f_angle_d 1.092
f_plane_restr 0.005
f_chiral_restr 0.072
f_dihedral_angle_d 14.152
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2015
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 180

Software

Software
Software Name Purpose
PHENIX refinement version: 1.7_650
PDB_EXTRACT data extraction version: 3.100
ADSC data collection version: Quantum
HKL-2000 data reduction
HKL-2000 data scaling
BALBES phasing