X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details PEG 3000, cacodylic acid, sodium glutamate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 255.26 α = 90
b = 265.25 β = 90
c = 184.4 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline

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
3 40 -- -- -- -- -- 241858 241858 -- -- --

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 3.0 40.0 -- 0.0 241858 241858 12042 -- 0.259 0.259 0.2575 0.2873 --
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 3.0 3.0775 -- 801 15875 0.347 0.381 -- --
X Ray Diffraction 3.077 3.1613 -- 844 16193 0.324 0.354 -- --
X Ray Diffraction 3.161 3.2523 -- 894 15772 0.308 0.33 -- --
X Ray Diffraction 3.252 3.3517 -- 795 15591 0.301 0.347 -- --
X Ray Diffraction 3.352 3.4609 -- 783 15051 0.286 0.331 -- --
X Ray Diffraction 3.461 3.5814 -- 736 14685 0.261 0.297 -- --
X Ray Diffraction 3.581 3.7154 -- 758 14133 0.255 0.286 -- --
X Ray Diffraction 3.715 3.8657 -- 732 13541 0.254 0.273 -- --
X Ray Diffraction 3.866 4.0359 -- 680 13104 0.24 0.265 -- --
X Ray Diffraction 4.036 4.2308 -- 645 12465 0.226 0.271 -- --
X Ray Diffraction 4.231 4.4568 -- 621 11837 0.222 0.263 -- --
X Ray Diffraction 4.457 4.7235 -- 600 11249 0.229 0.263 -- --
X Ray Diffraction 4.724 5.0447 -- 539 10561 0.24 0.27 -- --
X Ray Diffraction 5.045 5.4416 -- 520 9971 0.264 0.276 -- --
X Ray Diffraction 5.442 5.95 -- 515 9225 0.293 0.329 -- --
X Ray Diffraction 5.95 6.634 -- 445 8422 0.278 0.313 -- --
X Ray Diffraction 6.634 7.6254 -- 380 7511 0.216 0.237 -- --
X Ray Diffraction 7.625 9.2555 -- 333 6413 0.187 0.219 -- --
X Ray Diffraction 9.255 12.7523 -- 263 5092 0.191 0.206 -- --
X Ray Diffraction 12.752 40.0 -- 158 3125 0.388 0.373 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 2.458
Anisotropic B[1][1] -3.182
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.907
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.089
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.018
r_bond_refined_d 0.024
r_angle_refined_deg 2.034
r_dihedral_angle_1_deg 6.691
r_chiral_restr 0.122
r_gen_planes_refined 0.006
r_xyhbond_nbd_refined 0.172
r_metal_ion_refined 0.199
r_symmetry_vdw_refined 0.315
r_symmetry_hbond_refined 0.248
r_mcbond_it 0.236
r_mcangle_it 0.384
r_scbond_it 0.702
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 59080
Nucleic Acid Atoms 0
Heterogen Atoms 196
Solvent Atoms 181

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC5 (CCP4: Supported Program) version: refmac_5.1.19 refinement