3KXD | pdb_00003kxd

Crystal structure of the mthk rck in complex with cadmium

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	318	1M NH4-FORMATE, 10% PEG 4000, 0.1M NA ACETATE, PH 4.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 318K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.022	α = 90
b = 38.293	β = 95.1
c = 96.634	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	CCD	ADSC QUANTUM 315	FLAT MIRROR, RH COATED	2008-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1		SSRL	BL9-1

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	2.2	57.83	99.4	0.039	10.8	3.7		21805

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	FOURIER SYNTHESIS	THROUGHOUT	2AEJ	2.2	57.83	20697	1108	99.31	0.1878	0.1844	0.25	0.25364	0.31	RANDOM	51.557

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]
-1.1		-1.02	0.41		0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.503
r_dihedral_angle_3_deg	17.503
r_dihedral_angle_4_deg	15.556
r_dihedral_angle_1_deg	5.619
r_scangle_it	4.715
r_scbond_it	2.88
r_angle_refined_deg	1.877
r_mcangle_it	1.696
r_mcbond_it	0.962
r_mcbond_other	0.335
r_symmetry_hbond_refined	0.319
r_symmetry_vdw_other	0.313
r_metal_ion_refined	0.295
r_symmetry_vdw_refined	0.239
r_nbd_refined	0.235
r_nbd_other	0.21
r_xyhbond_nbd_refined	0.201
r_nbtor_refined	0.181
r_chiral_restr	0.14
r_nbtor_other	0.095
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_gen_planes_other	0.001
r_bond_other_d
r_angle_other_deg
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3378
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing