X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 293.0
Details 50MM SODIUM ACETATE, 2.4M SODIUM FORMATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.03 α = 90
b = 88.85 β = 90
c = 229.74 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV RIGAKU VARIMAX CONFOCAL OPTICS 2005-10-28
Diffraction Radiation
Monochromator Protocol
RIGAKU VARIMAX CONFOCAL OPTICS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 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
2.3 48.88 99.3 -- 0.089 -- 12.43 31445 31228 -- -- 31.6
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)
2.3 2.38 96.7 -- 0.206 9.5 7.98 3089

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 2.3 14.81 -- 0.0 31113 31099 3115 99.96 -- 0.16959 0.16383 0.22236 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 2.3 2.358 2150 207 1943 0.192 0.257 -- 99.86
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 28.921
Anisotropic B[1][1] 0.81
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.22
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 14.229
r_scbond_it 4.558
r_bond_refined_d 0.007
r_scangle_it 5.754
r_dihedral_angle_1_deg 5.58
r_dihedral_angle_2_deg 37.577
r_gen_planes_refined 0.003
r_symmetry_vdw_refined 0.15
r_symmetry_hbond_refined 0.152
r_mcbond_it 1.464
r_nbtor_refined 0.297
r_chiral_restr 0.07
r_mcangle_it 2.523
r_nbd_refined 0.185
r_xyhbond_nbd_refined 0.111
r_angle_refined_deg 1.108
r_dihedral_angle_4_deg 18.516
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.275
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4871
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 367

Software

Software
Software Name Purpose
AMoRE phasing
REFMAC refinement version: 5.2.0019
CrystalClear data collection
d*TREK data reduction
d*TREK data scaling