3H86 | pdb_00003h86

Crystal structure of adenylate kinase from Methanococcus maripaludis

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.7	273	3.4 M ammonium chloride, 0.1 M sodium acetate, 3% ethylene glycol (v/v)., pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.84	α = 90
b = 102.84	β = 90
c = 228.72	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	103	IMAGE PLATE	RIGAKU RAXIS IV	Rigaku Osmic Mirrors	2008-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.54

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	2.5	29.69	99.9	0.082	9.6	2.44	31194	31158		3

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)
	2.5	2.59	100		0.33	2.3	2.4	3109

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 (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 1KHT	2.5	19.7	31158	27970	3138	99.86	0.18821	0.18268	0.18	0.23911	0.21	RANDOM	59.467

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]
9.05			9.05		-18.1

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_2_deg	32.944
f_dihedral_angle_4_deg	20.369
f_dihedral_angle_3_deg	20.275
f_dihedral_angle_1_deg	7.119
f_scangle_it	4.547
f_scbond_it	3.002
f_angle_refined_deg	2.151
f_mcangle_it	1.995
f_mcbond_it	1.12
f_chiral_restr	0.124
f_bond_refined_d	0.022
f_gen_planes_refined	0.009
f_bond_other_d
f_angle_other_deg
f_gen_planes_other
f_nbd_refined
f_nbd_other
f_nbtor_refined
f_nbtor_other
f_xyhbond_nbd_refined
f_xyhbond_nbd_other
f_metal_ion_refined
f_metal_ion_other
f_symmetry_vdw_refined
f_symmetry_vdw_other
f_symmetry_hbond_refined
f_symmetry_hbond_other
f_symmetry_metal_ion_refined
f_symmetry_metal_ion_other
f_mcbond_other
f_rigid_bond_restr
f_sphericity_free
f_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5848
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	228

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling