X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 298.0
Details Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.17M Amm Acetate, 0.085 M Sodium Citrate pH 5.6, 25.5% Peg4000, 15% (V/V) glycerol); Cryoprotection (Reservoir taken to 20% glycerol), vapor diffusion, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.6 α = 90
b = 112.48 β = 90
c = 194.38 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 RAYONIX MX225HE MIRRORS 2012-10-16
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID

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
2.2 194.38 98.5 -- 0.175 -- 6.1 99618 99618 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)
2.2 2.32 97.9 0.7 0.7 1.1 6.1 14286

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 2.2 37.126 0.0 0.0 99532 99532 4984 98.2 -- 0.1592 0.1559 0.2234 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 2.2 2.225 -- 154 3082 0.2123 0.3011 -- 97.0
X Ray Diffraction 2.225 2.2512 -- 156 3111 0.2256 0.3067 -- 98.0
X Ray Diffraction 2.2512 2.2786 -- 175 3046 0.2118 0.2858 -- 98.0
X Ray Diffraction 2.2786 2.3075 -- 179 3107 0.2021 0.32 -- 98.0
X Ray Diffraction 2.3075 2.3378 -- 164 3091 0.2041 0.2714 -- 97.0
X Ray Diffraction 2.3378 2.3698 -- 157 3129 0.1896 0.2774 -- 98.0
X Ray Diffraction 2.3698 2.4037 -- 158 3086 0.1975 0.294 -- 97.0
X Ray Diffraction 2.4037 2.4396 -- 187 3111 0.205 0.2752 -- 98.0
X Ray Diffraction 2.4396 2.4777 -- 178 3062 0.1971 0.2919 -- 98.0
X Ray Diffraction 2.4777 2.5183 -- 147 3139 0.1963 0.2939 -- 98.0
X Ray Diffraction 2.5183 2.5617 -- 184 3088 0.19 0.2747 -- 98.0
X Ray Diffraction 2.5617 2.6083 -- 183 3116 0.178 0.2753 -- 98.0
X Ray Diffraction 2.6083 2.6584 -- 166 3110 0.1768 0.2612 -- 98.0
X Ray Diffraction 2.6584 2.7127 -- 164 3111 0.169 0.235 -- 98.0
X Ray Diffraction 2.7127 2.7716 -- 148 3147 0.1657 0.2833 -- 98.0
X Ray Diffraction 2.7716 2.8361 -- 166 3112 0.1636 0.255 -- 98.0
X Ray Diffraction 2.8361 2.907 -- 169 3128 0.1633 0.233 -- 98.0
X Ray Diffraction 2.907 2.9856 -- 165 3156 0.1644 0.2767 -- 98.0
X Ray Diffraction 2.9856 3.0734 -- 140 3148 0.1663 0.2323 -- 98.0
X Ray Diffraction 3.0734 3.1725 -- 155 3145 0.1613 0.2537 -- 98.0
X Ray Diffraction 3.1725 3.2858 -- 169 3176 0.1538 0.2291 -- 98.0
X Ray Diffraction 3.2858 3.4173 -- 170 3167 0.1423 0.2018 -- 98.0
X Ray Diffraction 3.4173 3.5727 -- 203 3122 0.1294 0.1732 -- 99.0
X Ray Diffraction 3.5727 3.7609 -- 166 3183 0.1235 0.1679 -- 98.0
X Ray Diffraction 3.7609 3.9963 -- 184 3156 0.1253 0.1802 -- 99.0
X Ray Diffraction 3.9963 4.3044 -- 161 3241 0.1227 0.1777 -- 99.0
X Ray Diffraction 4.3044 4.7368 -- 147 3254 0.1192 0.1693 -- 99.0
X Ray Diffraction 4.7368 5.4204 -- 154 3272 0.1235 0.1732 -- 100.0
X Ray Diffraction 5.4204 6.8222 -- 143 3346 0.1494 0.2269 -- 100.0
X Ray Diffraction 6.8222 37.1311 -- 192 3406 0.1619 0.1777 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.4895
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.636
f_plane_restr 0.005
f_chiral_restr 0.075
f_angle_d 1.018
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14481
Nucleic Acid Atoms 0
Heterogen Atoms 333
Solvent Atoms 1271

Software

Computing
Computing Package Purpose
UKNOWN Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
BALBES Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALA version: 3.3.20 data reduction
Mosflm data collection