X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 289.0
Details 20mM Sodium citrate Buffer, 20% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.85 α = 90
b = 32.53 β = 90.11
c = 72.38 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Mirrors 2000-02-21
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.00061 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
1.2 30 92.1 -- 0.038 -- 14.1 67242 67242 0.01 -3.0 12.9
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)
1.2 1.22 71.2 -- 0.226 -- 2.8 2545

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
FOURIER SYNTHESIS 1.2 29.36 -- 0.001 63814 63814 3421 92.9 0.19602 0.19431 0.19431 0.22824 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 1.204 1.236 3868 205 3868 0.261 0.277 -- 71.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.68
Anisotropic B[1][1] -0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.05
Anisotropic B[2][2] 0.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_symmetry_vdw_other 0.279
r_gen_planes_other 0.004
r_symmetry_vdw_refined 0.235
r_rigid_bond_restr 1.337
r_bond_refined_d 0.011
r_sphericity_bonded 2.701
r_dihedral_angle_1_deg 4.136
r_sphericity_free 2.409
r_xyhbond_nbd_other 0.231
r_scangle_it 3.54
r_gen_planes_refined 0.009
r_xyhbond_nbd_refined 0.269
r_symmetry_hbond_refined 0.295
r_angle_refined_deg 1.661
r_scbond_it 2.345
r_dihedral_angle_2_deg 12.842
r_nbd_refined 0.25
r_mcangle_it 1.927
r_chiral_restr 0.092
r_angle_other_deg 0.863
r_mcbond_it 1.233
r_nbd_other 0.222
r_nbtor_other 0.191
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1902
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 558

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
MAR345 data collection
SCALEPACK data scaling
CNS phasing