X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 283.0
Details PEG 10000, 1,6-hexanediol, DTT, HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.36 α = 90
b = 76.24 β = 103.7
c = 73.48 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2000-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.9801 ELETTRA 5.2R

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
2.54 70.71 -- 0.142 -- -- 12.3 17709 17709 -- 0.0 --

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 2.54 70.71 -- -- 17709 17709 965 98.22 -- 0.20068 0.19639 0.27887 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 2.54 2.606 -- 57 1179 0.246 0.384 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.781
Anisotropic B[1][1] 0.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.55
Anisotropic B[2][2] -0.91
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.98
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.163
r_nbd_refined 0.252
r_scangle_it 2.214
r_mcangle_it 2.295
r_scbond_it 1.399
r_angle_other_deg 1.104
r_symmetry_hbond_refined 0.361
r_gen_planes_other 0.006
r_symmetry_vdw_other 0.367
r_gen_planes_refined 0.007
r_chiral_restr 0.103
r_angle_refined_deg 1.836
r_mcbond_it 1.343
r_xyhbond_nbd_refined 0.211
r_nbtor_other 0.102
r_dihedral_angle_1_deg 7.547
r_nbd_other 0.27
r_bond_refined_d 0.02
r_bond_other_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4589
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 32

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
MAR345 data collection
SCALEPACK data scaling
AMoRE phasing