X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details 2.5M sodium chloride, 0.03M phosphate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57 α = 90
b = 61.8 β = 90
c = 34 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC double-mirror 2002-02-25
Diffraction Radiation
Monochromator Protocol
Ni FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
1.8 41.89 89.7 0.095 -- -- -- 27423 11117 -- -- --

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 1.81 41.89 -- -- -- 9777 504 89.65 -- 0.18407 0.18125 0.23759 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 1.809 1.856 -- 23 408 0.313 0.36 -- 52.31
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 14.698
Anisotropic B[1][1] -0.65
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.31
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 34.523
r_mcangle_it 1.484
r_dihedral_angle_1_deg 6.269
r_dihedral_angle_3_deg 15.453
r_symmetry_vdw_refined 0.296
r_scbond_it 2.689
r_bond_refined_d 0.015
r_mcbond_it 0.839
r_angle_refined_deg 1.541
r_xyhbond_nbd_refined 0.178
r_dihedral_angle_4_deg 16.632
r_nbtor_refined 0.292
r_chiral_restr 0.107
r_metal_ion_refined 0.117
r_symmetry_hbond_refined 0.18
r_gen_planes_refined 0.006
r_scangle_it 4.5
r_nbd_refined 0.223
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1029
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 116

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing