X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PEG 8K 3%, 100MM MES, 200MM CA-CACODYLATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.97 α = 90
b = 41.31 β = 90
c = 31.69 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER PROTEUM 300 -- 2005-05-15
Diffraction Radiation
Monochromator Protocol
SILICONE MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 6B 0.97940, 0.97952, 0.97962, 0.98742 PAL/PLS 6B

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
1.8 50 99.9 -- 0.099 -- 7.3 -- 11373 0.0 0.0 --
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)
1.8 1.86 100.0 -- 0.368 -- 7.2 --

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 1.8 44.5 -- 0.0 -- 10781 543 99.6 -- 0.208 0.206 0.24 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 1.8 1.85 -- 44 749 0.211 0.35 -- 96.35
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.15
Anisotropic B[1][1] -1.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.99
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.11
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_free 6.178
r_nbtor_refined 0.302
r_scbond_it 3.563
r_mcbond_it 1.564
r_nbd_refined 0.218
r_xyhbond_nbd_refined 0.176
r_dihedral_angle_2_deg 39.675
r_mcangle_it 2.189
r_symmetry_hbond_refined 0.184
r_angle_refined_deg 1.461
r_chiral_restr 0.096
r_dihedral_angle_3_deg 14.64
r_sphericity_bonded 3.007
r_scangle_it 4.617
r_gen_planes_refined 0.006
r_bond_refined_d 0.015
r_symmetry_vdw_refined 0.314
r_rigid_bond_restr 2.657
r_dihedral_angle_1_deg 5.433
r_dihedral_angle_4_deg 19.062
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 925
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 78

Software

Software
Software Name Purpose
SOLVE phasing
REFMAC refinement version: 5.2.0003
HKL-2000 data collection
DENZO data reduction
SCALEPACK data scaling