4JD0 | pdb_00004jd0

Structure of the inositol-1-phosphate CTP transferase from T. maritima.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QQX	PDB ENTRY 2QQX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	1.8 2.0 M ammonium phosphate and 100 mM LiCl buffered at pH 8.5 with 100 mM Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.91	68.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.09	α = 90
b = 133.09	β = 90
c = 43.365	γ = 120

Symmetry
Space Group	P 32 2 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	IMAGE PLATE	RIGAKU RAXIS HTC		2009-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-D	1.54

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	1.8	115.47	93	0.045	25.2	5	38500	38500

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	1.8	1.83	63.4		0.41		2.6	1287

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2QQX	1.8	115.47	38500	36573	1925	93.82	0.1141	0.11136	0.1104	0.16606	0.1659	RANDOM	31.767

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]
0.64	0.32		0.64		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	46.379
r_dihedral_angle_2_deg	29.757
r_sphericity_bonded	28.252
r_dihedral_angle_3_deg	15.36
r_dihedral_angle_4_deg	13.972
r_rigid_bond_restr	8.052
r_dihedral_angle_1_deg	6.493
r_angle_refined_deg	2.354
r_chiral_restr	0.153
r_bond_refined_d	0.024
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1939
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	50

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling