3SSQ | pdb_00003ssq

CcmK2 - form 1 dodecamer

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A1B	pdb entry 2A1B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	30 % PEG 2000 MME, 0.21 M (NH4)2SO4, 0.1 M Na acetate , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.362	α = 90
b = 83.362	β = 90
c = 226.86	γ = 90

Symmetry
Space Group	P 41 21 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	CCD	MARMOSAIC 225 mm CCD	White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM)	2008-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97934	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	40	99.5	0.05	14.2	7.1	41410	41410	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	98.4		0.525	2.5		4005

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 (All)	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 2A1B	2.2	40	41410	39066	2064	98.83	0.18907	0.18907	0.18663	0.19	0.2366	0.24	RANDOM	59.565

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]
1.75			1.75		-3.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.895
r_dihedral_angle_4_deg	19.633
r_dihedral_angle_3_deg	16.015
r_dihedral_angle_1_deg	6.082
r_scangle_it	2.036
r_scbond_it	1.423
r_angle_refined_deg	1.401
r_angle_other_deg	0.974
r_mcangle_it	0.776
r_mcbond_it	0.654
r_symmetry_vdw_refined	0.32
r_symmetry_vdw_other	0.232
r_nbd_other	0.195
r_xyhbond_nbd_refined	0.182
r_nbd_refined	0.181
r_nbtor_refined	0.161
r_symmetry_hbond_refined	0.131
r_mcbond_other	0.11
r_nbtor_other	0.086
r_chiral_restr	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4510
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MxDC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling