2ZKT | pdb_00002zkt

Structure of PH0037 protein from Pyrococcus horikoshii

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.6	295	18% PEG 20K, 0.1M Tris_Hcl, 0.5M licl2, pH 6.6, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.9	α = 90
b = 155.9	β = 90
c = 230.857	γ = 120

Symmetry
Space Group	H 3 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	graphite	2005-05-21	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.282247, 1.282786, 1.33	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	2.4	50	99.9	0.062	10.2	4.5	39490	39476			25.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.4	10	39474	2104	99.91	0.27749	0.27705	0.2698	0.28556	0.2701	RANDOM	55.521

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]
-0.14	-0.07		-0.14		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.563
r_dihedral_angle_4_deg	18.192
r_dihedral_angle_3_deg	15.137
r_scangle_it	5.24
r_scbond_it	3.364
r_dihedral_angle_1_deg	2.462
r_mcangle_it	1.961
r_angle_refined_deg	1.44
r_mcbond_it	1.248
r_symmetry_metal_ion_refined	0.613
r_symmetry_vdw_refined	0.331
r_nbtor_refined	0.324
r_nbd_refined	0.274
r_xyhbond_nbd_refined	0.197
r_symmetry_hbond_refined	0.15
r_chiral_restr	0.11
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5493
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms	6

Software

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