X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details 12-14 % PEG 6000, 150-300 MM NACL 25 MM HEPES PH 7-8, 10 MM MGCL2, 100-150 MICROM ADP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.49 α = 90
b = 91.81 β = 90
c = 260.05 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 2001-09-15
Diffraction Radiation
Monochromator Protocol
TRIANGULAR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- 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
2.4 22 98.4 0.089 -- -- 6.7 -- 82874 -- -- --
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)
2.4 2.44 86.1 0.614 -- 1.58 2.8 --

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 2.4 15.0 -- -- -- 80953 1604 98.2 -- 0.206 0.205 0.253 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 2.4 2.46 -- 112 5018 0.284 0.343 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.02
Anisotropic B[1][1] -2.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.8
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.16
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.362
r_mcangle_it 0.904
r_mcbond_it 0.469
r_nbd_refined 0.197
r_nbd_other 0.226
r_xyhbond_nbd_refined 0.173
r_nbtor_other 0.086
r_gen_planes_other 0.002
r_dihedral_angle_1_deg 6.2
r_bond_refined_d 0.012
r_symmetry_vdw_refined 0.177
r_scbond_it 1.439
r_symmetry_hbond_refined 0.134
r_bond_other_d 0.002
r_gen_planes_refined 0.004
r_chiral_restr 0.07
r_angle_other_deg 0.832
r_symmetry_vdw_other 0.238
r_scangle_it 2.416
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12171
Nucleic Acid Atoms 654
Heterogen Atoms 28
Solvent Atoms 380

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling