X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 297.0
Details 20 mM NaAcetate, 20% PEG 3000 + 4% PEG 600, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.87 α = 90
b = 43.87 β = 90
c = 238.31 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2004-05-26
Diffraction Radiation
Monochromator Protocol
Rigaku/MSC green optics SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.25 20 94.0 -- 0.044 -- 3.6 11307 11307 -- -3.0 --
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)
2.25 2.33 93.0 -- 0.439 2.1 -- --

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 2.3 19.92 -- 0.0 -- 10057 518 94.61 -- 0.23999 0.23682 0.29895 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 2.3 2.359 -- 32 673 0.328 0.561 -- 92.16
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.138
Anisotropic B[1][1] 0.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.28
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.788
r_dihedral_angle_1_deg 7.687
r_mcbond_it 1.015
r_bond_refined_d 0.018
r_nbtor_refined 0.315
r_xyhbond_nbd_refined 0.185
r_symmetry_vdw_refined 0.325
r_angle_refined_deg 2.191
r_scbond_it 2.563
r_gen_planes_refined 0.009
r_dihedral_angle_4_deg 18.005
r_chiral_restr 0.12
r_symmetry_hbond_refined 0.22
r_nbd_refined 0.252
r_scangle_it 3.853
r_dihedral_angle_2_deg 30.013
r_dihedral_angle_3_deg 19.284
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 961
Nucleic Acid Atoms 363
Heterogen Atoms 0
Solvent Atoms 82

Software

Software
Software Name Purpose
CrystalClear data collection version: (MSC/RIGAKU)
MOLREP phasing
REFMAC refinement version: 5.2
DENZO data reduction
SCALEPACK data scaling