X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 12% PEG 3350, 100mM Tris-HCl, 200mM ammonium acetate, 150mM NaCl, 100mM NDSB-256, pH 8.0, vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.71 α = 97.68
b = 105.69 β = 98.43
c = 126.82 γ = 100.31
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2013-11-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.000 SPRING-8 BL32XU

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
2.5 46.88 98.2 0.063 -- -- -- -- 130485 -- -3.0 59.84
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)
2.5 2.65 96.2 0.011 -- 2.1 -- --

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 2.5 46.701 -- 1.98 130396 130396 6521 98.53 0.2235 0.2235 0.2219 0.2536 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 2.5 2.5284 -- 219 4151 0.3414 0.3789 -- 98.0
X Ray Diffraction 2.5284 2.5582 -- 216 4100 0.3223 0.3575 -- 98.0
X Ray Diffraction 2.5582 2.5894 -- 216 4100 0.318 0.3414 -- 98.0
X Ray Diffraction 2.5894 2.6221 -- 215 4091 0.3158 0.3573 -- 98.0
X Ray Diffraction 2.6221 2.6566 -- 217 4127 0.3124 0.3438 -- 98.0
X Ray Diffraction 2.6566 2.693 -- 215 4068 0.2998 0.3239 -- 98.0
X Ray Diffraction 2.693 2.7315 -- 216 4110 0.2951 0.3468 -- 98.0
X Ray Diffraction 2.7315 2.7723 -- 217 4128 0.2912 0.3449 -- 98.0
X Ray Diffraction 2.7723 2.8156 -- 217 4125 0.2887 0.3274 -- 98.0
X Ray Diffraction 2.8156 2.8617 -- 217 4109 0.2781 0.3203 -- 98.0
X Ray Diffraction 2.8617 2.9111 -- 216 4098 0.2932 0.3091 -- 98.0
X Ray Diffraction 2.9111 2.964 -- 219 4169 0.2945 0.3288 -- 98.0
X Ray Diffraction 2.964 3.021 -- 217 4113 0.2877 0.3027 -- 98.0
X Ray Diffraction 3.021 3.0826 -- 218 4151 0.2786 0.3069 -- 99.0
X Ray Diffraction 3.0826 3.1497 -- 215 4091 0.2666 0.3017 -- 99.0
X Ray Diffraction 3.1497 3.2229 -- 219 4156 0.2584 0.3039 -- 99.0
X Ray Diffraction 3.2229 3.3035 -- 218 4148 0.2487 0.287 -- 99.0
X Ray Diffraction 3.3035 3.3928 -- 215 4085 0.2462 0.2745 -- 99.0
X Ray Diffraction 3.3928 3.4926 -- 220 4182 0.2434 0.2689 -- 99.0
X Ray Diffraction 3.4926 3.6053 -- 218 4134 0.2395 0.2652 -- 99.0
X Ray Diffraction 3.6053 3.7341 -- 218 4143 0.2204 0.2419 -- 99.0
X Ray Diffraction 3.7341 3.8835 -- 217 4132 0.2152 0.2595 -- 99.0
X Ray Diffraction 3.8835 4.0602 -- 220 4186 0.2075 0.2552 -- 99.0
X Ray Diffraction 4.0602 4.2741 -- 219 4154 0.1974 0.2368 -- 99.0
X Ray Diffraction 4.2741 4.5417 -- 218 4132 0.1907 0.2377 -- 99.0
X Ray Diffraction 4.5417 4.892 -- 218 4152 0.1844 0.1994 -- 99.0
X Ray Diffraction 4.892 5.3836 -- 219 4165 0.1881 0.2341 -- 99.0
X Ray Diffraction 5.3836 6.1612 -- 220 4171 0.1994 0.2253 -- 100.0
X Ray Diffraction 6.1612 7.7566 -- 220 4183 0.1949 0.2076 -- 100.0
X Ray Diffraction 7.7566 46.7096 -- 212 4021 0.1657 0.1874 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 80.5122
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.58
f_plane_restr 0.002
f_chiral_restr 0.022
f_angle_d 0.526
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 18997
Nucleic Acid Atoms 5012
Heterogen Atoms 0
Solvent Atoms 144

Software

Computing
Computing Package Purpose
BSS Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
PHENIX (phenix.refine: 1.8.3_1479) Structure Refinement
Software
Software Name Purpose
PDB_EXTRACT version: 3.14 data extraction
phenix refinement
Xscale data reduction