1WL8

Crystal structure of PH1346 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	1QDL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	4.8	295	Acetate, PEG, pH 4.8, microbatch, temperature 295.0K

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.808	α = 90
b = 63.48	β = 90
c = 65.161	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	RH COATED BENT-CYLINDRICAL MIRROR	2004-03-21	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	1.45	40	99.9	0.07	14.7	7	33392	33220			10.81

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)
	1.45	1.5	100		0.25

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1QDL	1.45	28.99	33392	33220	1758	99.83	0.15638	0.15638	0.15544	0.17365	RANDOM	9.924

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]
0.88			-0.21		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.637
r_scangle_it	4.032
r_scbond_it	2.457
r_mcangle_it	1.571
r_angle_refined_deg	1.481
r_angle_other_deg	0.856
r_mcbond_it	0.815
r_symmetry_vdw_other	0.282
r_nbd_refined	0.278
r_nbd_other	0.256
r_symmetry_vdw_refined	0.23
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.126
r_nbtor_other	0.092
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.009
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1504
Nucleic Acid Atoms
Solvent Atoms	215
Heterogen Atoms	1

Software

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