X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 295.0
Details sodium/potassium phosphate, sodium acetate, guanidine hydrochloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.91 α = 90
b = 74.13 β = 92.38
c = 105.2 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
CCD MARRESEARCH -- 2003-01-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 5ID-B 0.9479 APS 5ID-B

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
1.5 150 97.1 0.073 0.066 -- 4.4 424098 97263 0.0 0.0 14.4
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)
1.5 1.54 90.4 0.302 0.25 2.7 2.8 6308

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 1.5 105.41 -- -- -- 92370 4870 96.84 0.167 0.16702 0.1656 0.19427 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 1.5 1.539 -- 338 6308 0.211 0.236 -- 90.07
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.41
Anisotropic B[1][1] -0.69
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.38
Anisotropic B[2][2] -0.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.89
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.183
r_bond_other_d 0.001
r_gen_planes_other 0.001
r_scbond_it 2.044
r_nbtor_other 0.082
r_symmetry_vdw_refined 0.148
r_scangle_it 2.945
r_dihedral_angle_3_deg 11.962
r_dihedral_angle_4_deg 13.302
r_xyhbond_nbd_refined 0.136
r_symmetry_vdw_other 0.295
r_chiral_restr 0.069
r_nbd_other 0.182
r_bond_refined_d 0.01
r_nbd_refined 0.22
r_mcbond_it 1.082
r_mcangle_it 1.202
r_gen_planes_refined 0.005
r_dihedral_angle_1_deg 5.567
r_angle_other_deg 0.779
r_mcbond_other 0.18
r_angle_refined_deg 1.233
r_dihedral_angle_2_deg 33.878
r_symmetry_hbond_refined 0.136
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.042
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4120
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 597

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
XDS data reduction
CCP4 data scaling version: (SCALA)
AMoRE phasing