X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details soudium citrate, sodium potassium phosphate, sodium chrolide, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.75 α = 90
b = 120.75 β = 90
c = 239.15 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 310 -- 2003-08-17
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97 APS 19-ID

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
2.48 50 99.8 0.038 -- -- 11.3 37333 37232 -- -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)
2.48 2.57 100.0 0.749 -- 3.5 9.1 3657

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 2.48 50.0 -- 0.0 37232 35738 1494 99.73 0.21105 0.21105 0.2101 0.234 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 2.48 2.544 -- 103 2564 0.389 0.399 -- 99.44
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 64.054
Anisotropic B[1][1] -0.08
Anisotropic B[1][2] -0.04
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.12
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.117
r_symmetry_hbond_refined 0.163
r_angle_refined_deg 1.685
r_dihedral_angle_3_deg 19.327
r_dihedral_angle_2_deg 33.532
r_metal_ion_refined 0.184
r_dihedral_angle_1_deg 6.531
r_nbtor_refined 0.318
r_mcangle_it 1.429
r_symmetry_vdw_refined 0.195
r_nbd_refined 0.241
r_scbond_it 2.557
r_mcbond_it 0.741
r_dihedral_angle_4_deg 17.301
r_xyhbond_nbd_refined 0.128
r_scangle_it 3.975
r_bond_refined_d 0.019
r_gen_planes_refined 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.163
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3790
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 67

Software

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