X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 293.0
Details 60% Tacsimate pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.94 α = 90
b = 90.94 β = 90
c = 122.24 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD mirrors 2005-11-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 0.9184 APS 22-BM

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 50 99.0 0.11 0.092 -- 4.9 50259 49761 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)
2.2 2.28 92.4 0.532 -- 1.8 3.5 --

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 2.2 50.0 -- 0.0 -- 49718 2519 98.82 0.184 -- 0.181 0.231 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 2.2 2.258 3332 152 3180 0.235 0.307 -- 89.14
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.528
Anisotropic B[1][1] -0.97
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.97
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.93
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.877
r_scangle_it 4.37
r_nbtor_refined 0.309
r_xyhbond_nbd_refined 0.176
r_mcangle_it 1.867
r_nbd_refined 0.229
r_symmetry_hbond_refined 0.095
r_dihedral_angle_1_deg 6.477
r_gen_planes_refined 0.008
r_mcbond_it 1.164
r_dihedral_angle_3_deg 18.533
r_dihedral_angle_2_deg 38.304
r_dihedral_angle_4_deg 18.584
r_bond_refined_d 0.024
r_chiral_restr 0.129
r_symmetry_vdw_refined 0.268
r_scbond_it 2.978
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.298
Luzzati Resolution Cutoff (Low) 2.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5674
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 317

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 1.701