1KQP

NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS AT 1 A RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EE1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microgravity/vapor diffusion8.529825% PEG 400, 0.05M Tris, 0.05M MgCl2, 0.005M NaAD, 0.0025M ATP, pH 8.5, microgravity/vapor diffusion at 298K, microgravity/vapor diffusion
Crystal Properties
Matthews coefficientSolvent content
1.9736

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.28α = 90
b = 84.79β = 110.5
c = 59.64γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCH1998-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.9050EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.0283096.70.04832.83.4239033231200-1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.0281.0872.30.3812.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFREE R1EE11.0310421602617941410811830.10770.10630.10630.1354RANDOM
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
184272.095072.19
RMS Deviations
KeyRefinement Restraint Deviation
s_anti_bump_dis_restr0.149
s_non_zero_chiral_vol0.089
s_zero_chiral_vol0.083
s_approx_iso_adps0.068
s_similar_adp_cmpnt0.039
s_angle_d0.031
s_from_restr_planes0.0282
s_bond_d0.015
s_rigid_bond_adp_cmpnt0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4264
Nucleic Acid Atoms
Solvent Atoms714
Heterogen Atoms195

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement