X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8
Details 1.8 M LI2SO4, 100MM TRIS, 1MM MNCL, 10 MM BETAINE, 10% 2-METHYL-2,4-PENTANDIOLE, pH 8.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.69 α = 90
b = 97.69 β = 90
c = 312.05 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS, TRIANGULAR MONOCHROMATOR 2002-11-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, HAMBURG BW7B

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
2.1 30 95.1 0.069 -- -- 3.2 -- 89316 -- 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)
2.1 2.18 95.6 0.267 -- 4.7 3.3 --

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 2.1 19.96 -- -- -- 80645 4255 95.3 -- 0.159 0.156 0.205 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 2.1 2.15 -- 312 5849 0.191 0.246 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.26
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.709
r_scbond_it 2.933
r_mcangle_it 1.754
r_mcbond_it 0.97
r_nbd_refined 0.208
r_gen_planes_other 0.012
r_gen_planes_refined 0.01
r_chiral_restr 0.114
r_dihedral_angle_1_deg 6.581
r_angle_other_deg 0.922
r_angle_refined_deg 1.743
r_bond_other_d 0.002
r_bond_refined_d 0.022
r_nbd_other 0.252
r_nbtor_other 0.089
r_xyhbond_nbd_refined 0.201
r_symmetry_vdw_refined 0.181
r_symmetry_vdw_other 0.291
r_symmetry_hbond_refined 0.239
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8194
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 916

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE, BEAST Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement
BEAST model building
AMORE model building