2DVP | pdb_00002dvp

Structure of NTPase from Pyroccous horikoshii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V7R	PDB ENTRY 1V7R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	4.6	295	NaCl, acetate, pH 4.6, microbatch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.516	α = 90
b = 71.516	β = 90
c = 78.35	γ = 120

Symmetry
Space Group	P 31 1 2

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 V		2004-02-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0	SPring-8	BL26B1

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	1.9	50	96.2	0.046	20.8	7	17606	16658			23

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	99.3

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 1V7R	1.9	40	17606	16658	901	96.14	0.244	0.244	0.2495	0.27623	0.2508	RANDOM	50.22

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]
1.3	0.65		1.3		-1.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.339
r_dihedral_angle_4_deg	17.942
r_dihedral_angle_3_deg	16.027
r_dihedral_angle_1_deg	5.746
r_scangle_it	3.452
r_scbond_it	2.316
r_mcangle_it	1.497
r_angle_refined_deg	1.325
r_mcbond_it	0.949
r_nbtor_refined	0.319
r_nbd_refined	0.241
r_symmetry_vdw_refined	0.235
r_xyhbond_nbd_refined	0.191
r_symmetry_hbond_refined	0.102
r_chiral_restr	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1480
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing