2IT1 | pdb_00002it1

Structure of PH0203 protein from Pyrococcus horikoshii

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.1	295	20% PEG 4000, 0.5M LI2SO4, pH 8.1, microbatch, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.23	α = 90
b = 85.319	β = 97.16
c = 82.598	γ = 90

Symmetry
Space Group	P 1 21 1

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		2006-10-12	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS V		2006-04-16	M	MAD

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	0.979103, 0.9794, 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	1.94	50	98	0.046	12.9	6.6	47216	46653			26.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.94	2.01	98

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.94	20	47216	46653	2494	98.14	0.21	0.21	0.22	0.25	0.22	RANDOM	29.143

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]
-1.9		2.5	0.76		1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.153
r_dihedral_angle_3_deg	15.421
r_dihedral_angle_4_deg	10.95
r_dihedral_angle_1_deg	5.797
r_scangle_it	2.701
r_scbond_it	1.952
r_angle_refined_deg	1.358
r_mcangle_it	1.291
r_mcbond_it	1.148
r_angle_other_deg	0.846
r_symmetry_vdw_other	0.221
r_nbd_refined	0.213
r_nbd_other	0.195
r_symmetry_hbond_refined	0.191
r_nbtor_refined	0.178
r_symmetry_vdw_refined	0.175
r_mcbond_other	0.172
r_xyhbond_nbd_refined	0.152
r_nbtor_other	0.086
r_chiral_restr	0.077
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5754
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	5

Software

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