9QDT | pdb_00009qdt

Cytochrome c peroxidase YhjA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HQ6	CcpA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.8 M Na/K tartrate 100 mM HEPES/NaOH 2.5 mM Na2S2O4

Crystal Properties
Matthews coefficient	Solvent content
5.1	76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.42	α = 90
b = 101.42	β = 90
c = 134.68	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	ADSC QUANTUM 315		2010-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9393	ESRF	ID14-1

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	2.57	82	100	0.139	0.037	0.999	17.1	15.4		23032	2		54

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	2.57	2.69	100		1.363	0.359	0.785	2.6	15.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.572	81.149	22976	1185	99.952	0.175	0.1724	0.2042	0.2219	0.2484	40.199

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]
-0.266			-0.266		0.533

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.428
r_dihedral_angle_6_deg	14.611
r_dihedral_angle_2_deg	7.899
r_dihedral_angle_1_deg	7.175
r_lrange_it	7.125
r_lrange_other	7.081
r_scangle_it	5.775
r_scangle_other	5.638
r_mcangle_it	4.371
r_mcangle_other	4.371
r_scbond_it	3.752
r_scbond_other	3.648
r_mcbond_it	2.919
r_mcbond_other	2.919
r_angle_refined_deg	1.954
r_angle_other_deg	0.644
r_nbd_refined	0.298
r_symmetry_nbd_other	0.214
r_symmetry_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.169
r_nbd_other	0.141
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.085
r_symmetry_nbd_refined	0.077
r_metal_ion_refined	0.071
r_xyhbond_nbd_other	0.016
r_gen_planes_refined	0.01
r_gen_planes_other	0.01
r_bond_refined_d	0.008
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3268
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	152

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing