X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 303.0
Details 0.2M NaCl, 0.1M Magnesium Formate, 0.1M Sodium Acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.16 α = 90
b = 127.29 β = 90
c = 140.42 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-02-15
Diffraction Radiation
Monochromator Protocol
double flat Si crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 0.990 NSLS X25

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
3.4 50 99.8 0.047 0.047 -- 8.0 33298 33091 1.45 2.0 --
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)
3.4 3.55 99.8 0.01 -- 2.0 8.0 --

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 3.4 50.0 -- -- 28497 28441 1510 99.74 -- 0.26554 0.26399 0.29469 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 3.4 3.583 -- 202 4089 0.364 0.379 -- 99.91
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 111.263
Anisotropic B[1][1] 2.1
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.99
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.11
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.144
r_scbond_it 1.85
r_mcangle_it 3.414
r_mcbond_it 2.006
r_nbd_refined 0.241
r_gen_planes_refined 0.003
r_chiral_restr 0.078
r_dihedral_angle_4_deg 19.786
r_dihedral_angle_3_deg 20.111
r_dihedral_angle_2_deg 37.679
r_dihedral_angle_1_deg 5.15
r_angle_refined_deg 1.453
r_bond_refined_d 0.009
r_nbtor_refined 0.305
r_xyhbond_nbd_refined 0.145
r_symmetry_vdw_refined 0.308
r_symmetry_hbond_refined 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5672
Nucleic Acid Atoms 2844
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement