X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details 10.5 % PEG 5000 MME, 0.1 M MES pH 5.5, 0.05 ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.93 α = 90
b = 118.09 β = 90
c = 123.68 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
CCD MAR CCD 165 mm -- 2004-01-29
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.00033 SLS X06SA

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 40 98.58 0.056 -- -- 7.53 68942 68942 -- -- --
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)
2.2 2.28 97.1 0.401 -- -- 6.25 6728

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
FOURIER SYNTHESIS 2.21 40.0 -- -- 65406 65406 3477 98.58 0.19965 0.19965 0.19744 0.24186 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 2.21 2.263 -- 268 4633 0.237 0.313 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.122
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.59
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.01
r_angle_other_deg 1.035
r_scangle_it 3.245
r_dihedral_angle_4_deg 15.827
r_dihedral_angle_3_deg 15.245
r_nbd_refined 0.215
r_bond_refined_d 0.019
r_dihedral_angle_1_deg 6.544
r_chiral_restr 0.092
r_xyhbond_nbd_refined 0.17
r_symmetry_vdw_refined 0.233
r_dihedral_angle_2_deg 38.392
r_gen_planes_refined 0.008
r_nbd_other 0.19
r_symmetry_vdw_other 0.256
r_symmetry_hbond_refined 0.24
r_scbond_it 2.297
r_nbtor_other 0.092
r_bond_other_d 0.002
r_angle_refined_deg 1.594
r_mcbond_it 1.217
r_mcangle_it 1.664
r_mcbond_other 0.236
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.199
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8274
Nucleic Acid Atoms 0
Heterogen Atoms 156
Solvent Atoms 266

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.9999
DENZO data reduction
SCALEPACK data scaling
REFMAC phasing