X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.4
Details 1.4 M NAH2PO4, 0.35 M K2HPO4, 0.6% PEG 150, SITTING DROP, pH 4.40

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.65 α = 90
b = 61.65 β = 90
c = 116.02 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD -- 2003-04-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B -- NSLS X9B

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 30 100.0 0.07 -- -- 8.8 -- 6002 -- 0.0 36.9
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)
2.0 2.28 100.0 0.48 -- 4.6 8.8 --

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 2.2 40.0 -- -- -- 5996 581 99.9 -- 0.179 0.173 0.237 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 9.57 40.0 -- 9 85 0.238 0.304 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.52
Anisotropic B[1][1] -0.247
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.247
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.495
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.004
r_scangle_it 2.968
r_dihedral_angle_1_deg 5.438
r_nbtor_refined 0.302
r_xyhbond_nbd_refined 0.182
r_bond_refined_d 0.011
r_symmetry_hbond_refined 0.248
r_nbd_refined 0.187
r_dihedral_angle_4_deg 16.199
r_mcbond_it 0.616
r_chiral_restr 0.121
r_angle_refined_deg 2.525
r_mcangle_it 1.118
r_scbond_it 1.889
r_dihedral_angle_2_deg 34.403
r_dihedral_angle_3_deg 12.575
r_symmetry_vdw_refined 0.214
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 781
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 101

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
HKL-2000 data reduction
HKL-2000 data scaling
AMoRE phasing