2DM9

Crystal Structure of PH1978 from Pyrococcus horikoshii OT3

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.5	295	PEG 4000, CHES, pH 8.5, microbatch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.6	28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.196	α = 90
b = 55.317	β = 90
c = 77.481	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	RH coated bent-cylindrical mirror	2004-02-28	M	SINGLE WAVELENGTH
2	1	x-ray		IMAGE PLATE	RIGAKU RAXIS V		2004-05-29	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0	SPring-8	BL26B1
2	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0, 0.97946, 0.97914	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	1.85	40	98.8	0.065	11.6	4.7	18717	18477			20.03

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)
1,2	1.85	1.92	99.8		0.277

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.85	27.66	18717	18477	993	98.75	0.219	0.219	0.259	RANDOM	19.351

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]
-1.09			1.66		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	4.899
r_scangle_it	3.019
r_scbond_it	1.656
r_angle_other_deg	1.068
r_mcangle_it	1.011
r_angle_refined_deg	0.96
r_mcbond_it	0.514
r_symmetry_vdw_other	0.299
r_nbd_other	0.219
r_nbd_refined	0.187
r_symmetry_hbond_refined	0.146
r_xyhbond_nbd_refined	0.125
r_symmetry_vdw_refined	0.114
r_nbtor_other	0.081
r_chiral_restr	0.052
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1874
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms

Software

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