2IT3 | pdb_00002it3

Structure of PH1069 protein from Pyrococcus horikoshii

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.6	295	MES, NaCl, pH 6.6, microbatch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.673	α = 90
b = 57.951	β = 90
c = 167.416	γ = 90

Symmetry
Space Group	P 21 21 21

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		2006-04-12	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	2.1	50	99.7	0.079	9	6.5	22932	22800			29.1

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	2.1	2.18	99.7

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	2DRV	2.1	20	22800	21932	1162	99	0.24	0.24	0.2366	0.27	0.2744	RANDOM	37.693

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]
1.75			-2.05		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.269
r_dihedral_angle_4_deg	20.251
r_dihedral_angle_3_deg	14.033
r_scangle_it	5.286
r_scbond_it	3.481
r_mcangle_it	2.086
r_dihedral_angle_1_deg	1.632
r_mcbond_it	1.517
r_angle_refined_deg	1.352
r_nbtor_refined	0.327
r_symmetry_vdw_refined	0.283
r_nbd_refined	0.253
r_symmetry_hbond_refined	0.25
r_xyhbond_nbd_refined	0.22
r_chiral_restr	0.091
r_bond_refined_d	0.007
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3176
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms

Software

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