X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 298.0
Details 0.1M Sodium acetate trihydrate, 10%(w/v) Polyethylene glycol 1000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.42 α = 90
b = 106.09 β = 90
c = 46.95 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2010-11-15
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(III) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPRING-8 BL44XU

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
1.8 30 96.4 -- 0.091 -- 5.4 44147 44147 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)
1.8 1.83 100.0 -- 0.362 8.6 5.8 2239

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 1.8 28.515 -- 1.33 43648 43648 2201 96.0 -- 0.2128 0.211 0.2475 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 1.8 1.8391 -- 134 2653 0.2417 0.3105 -- 100.0
X Ray Diffraction 1.8391 1.8819 -- 147 2652 0.2377 0.2801 -- 100.0
X Ray Diffraction 1.8819 1.929 -- 101 2020 0.368 0.4615 -- 77.0
X Ray Diffraction 1.929 1.9811 -- 113 2545 0.2303 0.3127 -- 95.0
X Ray Diffraction 1.9811 2.0394 -- 144 2678 0.1873 0.2106 -- 100.0
X Ray Diffraction 2.0394 2.1052 -- 146 2642 0.1889 0.2402 -- 100.0
X Ray Diffraction 2.1052 2.1804 -- 137 2659 0.1982 0.2355 -- 100.0
X Ray Diffraction 2.1804 2.2677 -- 130 2206 0.2542 0.3051 -- 83.0
X Ray Diffraction 2.2677 2.3708 -- 152 2538 0.2056 0.2363 -- 95.0
X Ray Diffraction 2.3708 2.4958 -- 144 2673 0.1927 0.2392 -- 100.0
X Ray Diffraction 2.4958 2.652 -- 126 2700 0.215 0.2838 -- 99.0
X Ray Diffraction 2.652 2.8566 -- 141 2674 0.2149 0.2419 -- 99.0
X Ray Diffraction 2.8566 3.1438 -- 153 2703 0.2065 0.2203 -- 99.0
X Ray Diffraction 3.1438 3.5979 -- 132 2693 0.1944 0.2335 -- 98.0
X Ray Diffraction 3.5979 4.5301 -- 143 2634 0.1792 0.228 -- 96.0
X Ray Diffraction 4.5301 28.5187 -- 158 2777 0.2111 0.205 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.7143
Anisotropic B[1][1] 1.8496
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.8387
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.0109
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.587
f_plane_restr 0.004
f_chiral_restr 0.075
f_angle_d 1.0
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3218
Nucleic Acid Atoms 118
Heterogen Atoms 3
Solvent Atoms 632

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
AMoRE Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
AMoRE model building
HKL-2000 data collection