7FBY | pdb_00007fby

Crystal Structure of PH0140 from Pyrococcus horikosii OT3

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	0.1 M HEPES (PH 7.5), 4.3 M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.79	α = 90
b = 102.79	β = 90
c = 69.183	γ = 90

Symmetry
Space Group	I 4 2 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 RAXIS IV++		2019-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54178

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	35	99.9	0.087	32.54	9.2		12806

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	2.07			0.66

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2CYY	2.001	25.711	12806	646	99.86	0.175	0.1733	0.18	0.2122	0.21	30.418

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]
-0.261			-0.261		0.523

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.452
r_dihedral_angle_4_deg	18.291
r_dihedral_angle_3_deg	15.144
r_dihedral_angle_1_deg	6.303
r_lrange_it	5.731
r_lrange_other	5.729
r_scangle_it	4.071
r_scangle_other	4.069
r_mcangle_it	2.879
r_mcangle_other	2.877
r_scbond_it	2.736
r_scbond_other	2.734
r_mcbond_it	1.961
r_mcbond_other	1.959
r_angle_refined_deg	1.939
r_angle_other_deg	1.429
r_nbd_refined	0.281
r_symmetry_nbd_refined	0.269
r_nbd_other	0.214
r_symmetry_nbd_other	0.209
r_xyhbond_nbd_refined	0.193
r_symmetry_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.168
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1207
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	17

Software

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