X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 295.0
Details PEG 4000, ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.66 α = 90
b = 48.66 β = 90
c = 82.12 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH mirrors 2003-02-10
Diffraction Radiation
Monochromator Protocol
double Si(111) crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.0500, 1.2828 MPG/DESY, HAMBURG BW6

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
1.95 50 97.0 -- 0.042 -- 4.6 7120 6907 -- 1.0 52.6
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)
1.95 2.0 99.7 -- 0.447 6.3 -- --

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 2.0 15.0 -- 2.0 6775 6590 322 97.27 -- 0.24204 0.24083 0.26691 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 2.0 2.052 -- 24 475 0.296 0.337 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.879
Anisotropic B[1][1] 0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.834
r_gen_planes_other 0.002
r_nbtor_other 0.085
r_nbd_refined 0.213
r_bond_other_d 0.002
r_symmetry_vdw_refined 0.197
r_bond_refined_d 0.009
r_nbd_other 0.234
r_symmetry_vdw_other 0.196
r_angle_refined_deg 1.206
r_gen_planes_refined 0.005
r_chiral_restr 0.066
r_mcangle_it 3.556
r_dihedral_angle_1_deg 6.175
r_xyhbond_nbd_refined 0.219
r_symmetry_hbond_refined 0.135
r_scangle_it 5.211
r_scbond_it 3.259
r_mcbond_it 1.979
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 642
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 56

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
MLPHARE phasing
CNS refinement version: 1.0
REFMAC refinement version: 5.1
HKL-2000 data reduction