X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 9
Temperature 293.0
Details 0.1M Na-bicine pH 9, 2.6M Na-malonate pH 7, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.24 α = 90
b = 41.24 β = 104.43
c = 71.95 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ Osmic mirrors 2010-03-13
Diffraction Radiation
Monochromator Protocol
0.5 mm SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
1.7 21.1 99.9 0.045 0.045 -- 9.4 26720 26639 0.0 0.0 16.0
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)
1.7 1.79 99.3 0.185 0.185 10.7 8.8 3843

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 1.7 21.1 0.0 0.0 26628 26628 2678 99.89 0.167 0.167 0.162 0.215 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 1.7 1.744 -- 182 1725 0.299 0.479 -- 98.55
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 14.065
Anisotropic B[1][1] 0.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.03
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.18
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 20.531
r_dihedral_angle_2_deg 35.407
r_xyhbond_nbd_refined 0.162
r_dihedral_angle_1_deg 6.865
r_nbd_refined 0.221
r_symmetry_hbond_refined 0.195
r_angle_refined_deg 2.234
r_chiral_restr 0.171
r_scbond_it 3.258
r_dihedral_angle_3_deg 13.358
r_bond_refined_d 0.029
r_mcangle_it 2.204
r_scangle_it 4.848
r_mcbond_it 1.467
r_nbtor_refined 0.309
r_metal_ion_refined 0.052
r_gen_planes_refined 0.014
r_symmetry_vdw_refined 0.251
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2049
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 280

Software

Software
Software Name Purpose
REFMAC refinement
MOSFLM data reduction
SCALA data scaling version: 3.2.19
PDB_EXTRACT data extraction version: 3.006
O model building