2WR8 | pdb_00002wr8

Structure of Pyrococcus horikoshii SAM hydroxide adenosyltransferase in complex with SAH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WU8	PDB ENTRY 1WU8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		19.83% PEG 6000, 0.26M KCL, 0.1M MOPS PH 7

Crystal Properties
Matthews coefficient	Solvent content
1	41.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.561	α = 90
b = 65.561	β = 90
c = 142.685	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD	TORODIAL FOCUSING MIRROR	2008-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.77	50	99.7	0.04	11.4	4.6		22346		2

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	1.77	1.83	100		0.5	3.6	3.7

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 (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	PDB ENTRY 1WU8	1.77	52.78	21127	1137	99.66	0.17039	0.16796	0.1727	0.21739	0.2154	RANDOM	33.439

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]
-1.57	-0.78		-1.57		2.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.946
r_dihedral_angle_4_deg	17.436
r_dihedral_angle_3_deg	13.528
r_dihedral_angle_1_deg	6.654
r_scangle_it	3.117
r_scbond_it	2.331
r_angle_refined_deg	1.623
r_mcangle_it	1.301
r_mcbond_it	1.146
r_angle_other_deg	0.959
r_symmetry_vdw_other	0.266
r_mcbond_other	0.261
r_symmetry_vdw_refined	0.219
r_nbd_refined	0.212
r_nbd_other	0.211
r_nbtor_refined	0.186
r_symmetry_hbond_refined	0.163
r_xyhbond_nbd_refined	0.15
r_nbtor_other	0.109
r_chiral_restr	0.098
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2031
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	26

Software

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