2ZD2 | pdb_00002zd2

D202K mutant of P. denitrificans Atp12p

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P4X	PDB ENTRY 2P4X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	278	12% PEG 4000, 100mM Hepes-Na, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.16	α = 102.91
b = 51.047	β = 105.45
c = 67.117	γ = 90.07

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	MARMOSAIC 300 mm CCD		2007-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97924	APS	21-ID-F

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	1.8	50	97.5	0.082	15.3	3.8	48230	48230			20.7

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	1.8	1.83	95.6		0.555	2.269	3.1	2304

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 2P4X	1.8	35.21	46717	4716	93.9	0.225	0.225	0.23	0.279	0.28	RANDOM	28.8

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]
-0.87	-0.59	-0.27	-2.62	0.75	3.49

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.7
c_scangle_it	5.06
c_scbond_it	3.78
c_mcangle_it	3.3
c_mcbond_it	2.53
c_angle_deg	1.4
c_improper_angle_d	1.01
c_bond_d	0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3642
Nucleic Acid Atoms
Solvent Atoms	534
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
Accel	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing