X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 297.0
Details 0.4 M (NH4)2SO4, 0.9 M Li2SO4, and 0.1 M sodium citrate at pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 170.41 α = 90
b = 351.97 β = 90
c = 101.97 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2006-01-01
Diffraction Radiation
Monochromator Protocol
Double crystal, paralell (Si 111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL1-5 1.00 SSRL BL1-5

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
2.62 40 90.04 0.085 -- -- 4.5 -- 92718 2.0 2.0 --
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)
2.62 2.71 71.0 0.476 -- -- -- --

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 2.62 40.0 -- 1.5 79045 83222 4177 90.04 0.1881 0.18807 0.18601 0.22733 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 2.62 2.686 -- 236 4553 0.371 0.365 -- 70.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.371
Anisotropic B[1][1] 5.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.47
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 17.464
r_nbtor_refined 0.198
r_angle_other_deg 0.934
r_scbond_it 1.452
r_mcangle_it 1.05
r_bond_refined_d 0.015
r_symmetry_vdw_refined 0.17
r_symmetry_vdw_other 0.196
r_nbd_refined 0.223
r_scangle_it 2.274
r_dihedral_angle_2_deg 37.632
r_angle_refined_deg 1.499
r_dihedral_angle_3_deg 17.645
r_nbtor_other 0.091
r_symmetry_hbond_refined 0.217
r_metal_ion_refined 0.075
r_xyhbond_nbd_refined 0.152
r_gen_planes_other 0.001
r_bond_other_d 0.001
r_mcbond_it 0.626
r_chiral_restr 0.116
r_mcbond_other 0.094
r_dihedral_angle_1_deg 8.512
r_gen_planes_refined 0.004
r_nbd_other 0.194
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10771
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 406

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing