4Z9M | pdb_00004z9m

Crystal structure of human sarcomeric mitochondrial creatine kinase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GL6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	291	17% PEG-3350, 10mM DTT, 0.2M diammonium citrate, 0.1M Bis-TRIS, protein buffer also contained magnesium chloride, creatine, ADP

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.057	α = 70.12
b = 106.058	β = 84.57
c = 114.932	γ = 68.61

Symmetry
Space Group	P 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 210		2006-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00003	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	49.09	95.4	0.077	0.077	0.995	8.5	2		247985

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	95.5		0.897	0.894	0.318	1	2	12346

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		THROUGHOUT	2GL6	2.1	40	214294	4357	95.4	0.203	0.2023	0.21	0.2362	0.24	THIN SHELLS (SFTOOLS)	38.291

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]
-0.6	0.37	-0.84	-0.14	-0.49	0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.673
r_dihedral_angle_4_deg	16.369
r_dihedral_angle_3_deg	12.095
r_dihedral_angle_1_deg	5.749
r_mcangle_it	3.829
r_mcbond_it	2.49
r_mcbond_other	2.49
r_angle_refined_deg	1.267
r_angle_other_deg	0.903
r_chiral_restr	0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.673
r_dihedral_angle_4_deg	16.369
r_dihedral_angle_3_deg	12.095
r_dihedral_angle_1_deg	5.749
r_mcangle_it	3.829
r_mcbond_it	2.49
r_mcbond_other	2.49
r_angle_refined_deg	1.267
r_angle_other_deg	0.903
r_chiral_restr	0.069
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21843
Nucleic Acid Atoms
Solvent Atoms	849
Heterogen Atoms	306

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.