Experiment: 4K2I

Crystal structure of ntda from bacillus subtilis with bound cofactor pmp

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4K2B	PDB entry 4K2B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6	295	0.1M tri-sodium citrate, 0.2M ammonium acetate, 20% PEG3350, 55mM glutamate, microbatch, pH 5.6, EVAPORATION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.109	α = 90
b = 106.979	β = 95.96
c = 99.177	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	MIRRORS	2011-10-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1		CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.71	46.8	99.3	0.066	14.28	4		108740		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.71	1.75	98.5		0.755	2.14

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 4K2B	2.225	37.032	1.34	188767	50673	2599	99.32	0.1608	0.1581	0.1541	0.2112	0.2049

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]
-1.2584		2.5991	-3.2321		4.4905

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.514
f_angle_d	1.081
f_chiral_restr	0.075
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7008
Nucleic Acid Atoms
Solvent Atoms	585
Heterogen Atoms	84

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling