X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 293.0
Details PEG 550 MME, NaCl, DTT, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.03 α = 90
b = 100.03 β = 90
c = 103.23 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2002-09-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8841 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
1.75 30 98.6 -- 0.108 -- 4.8 -- 50437 0.0 0.0 23.87
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)
1.75 1.81 86.5 -- 0.426 3.0 3.2 4392

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
MAD 1.76 29.23 0.0 0.0 -- 44306 2366 92.93 -- 0.16421 0.16298 0.18715 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 1.76 1.806 2924 157 2924 0.192 0.258 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 22.531
Anisotropic B[1][1] 0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.18
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.104
r_bond_refined_d 0.013
r_symmetry_hbond_refined 0.152
r_angle_refined_deg 1.379
r_symmetry_vdw_other 0.294
r_scbond_it 2.538
r_angle_other_deg 1.538
r_gen_planes_other 0.005
r_xyhbond_nbd_refined 0.167
r_scangle_it 4.304
r_symmetry_vdw_refined 0.192
r_mcbond_it 1.055
r_nbd_refined 0.221
r_dihedral_angle_1_deg 5.431
r_nbd_other 0.239
r_mcangle_it 1.969
r_gen_planes_refined 0.006
r_bond_other_d 0.002
r_chiral_restr 0.089
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2586
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 316

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing
REFMAC refinement version: 5.1.19