X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details PEG 8000, lithium sulfate, Tris-HCl, 8-azaxanthine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.39 α = 90
b = 144.41 β = 90
c = 78.79 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2001-09-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.900 SPring-8 BL41XU

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
2.2 48.01 97.0 0.066 -- -- 6.0 75717 75560 -- 3.0 39.0
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)
2.2 2.257 90.0 0.066 0.189 2.1 5.3 10109

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 2.2 48.01 -- -- 75717 71917 3800 97.16 0.219 0.18232 0.18042 0.21806 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 2.2 2.257 -- 253 4775 0.214 0.275 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.968
Anisotropic B[1][1] -0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.07
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.212
r_gen_planes_other 0.008
r_mcangle_it 3.588
r_chiral_restr 0.087
r_angle_other_deg 3.193
r_scangle_it 3.758
r_angle_refined_deg 1.503
r_dihedral_angle_1_deg 5.651
r_symmetry_vdw_refined 0.265
r_symmetry_vdw_other 0.295
r_bond_refined_d 0.019
r_bond_other_d 0.0
r_nbd_other 0.284
r_mcbond_it 2.281
r_symmetry_hbond_refined 0.258
r_scbond_it 2.367
r_gen_planes_refined 0.006
r_nbtor_other 0.102
r_nbd_refined 0.217
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.263
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9892
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 409

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling
MOLREP phasing
REFMAC refinement version: 5.1.24
CCP4 data scaling version: (SCALA)