9GTA | pdb_00009gta

Reprocessing and re-refinement of Damage Free Ferric State of Dye Type Peroxidase Aa from Streptomyces lividans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6I43

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	PEG 6K, HEPES 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.7	α = 90
b = 68.2	β = 105.6
c = 74.6	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	301	CCD	MPCCD		2017-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL2	1.24	SACLA	BL2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Split (All)	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	1.86	40	100	0.105	7.8	392		59164

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.91			0.416

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.86	35.476	59136	3135	99.953	0.146	0.1446	0.1568	0.1722	0.1829	RANDOM	26.839

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]
-0.026		0.032	-0.014		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.358
r_dihedral_angle_3_deg	13.981
r_lrange_it	11.396
r_lrange_other	10.589
r_dihedral_angle_2_deg	8.508
r_dihedral_angle_1_deg	6.524
r_scangle_it	5.998
r_scangle_other	5.998
r_scbond_other	3.875
r_scbond_it	3.874
r_mcangle_other	3.179
r_mcangle_it	3.177
r_mcbond_it	2.341
r_mcbond_other	2.322
r_angle_refined_deg	1.579
r_angle_other_deg	0.543
r_xyhbond_nbd_refined	0.332
r_symmetry_xyhbond_nbd_refined	0.32
r_symmetry_nbd_refined	0.289
r_nbd_other	0.213
r_nbd_refined	0.212
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.181
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5534
Nucleic Acid Atoms
Solvent Atoms	540
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystFEL	data scaling
CrystFEL	data reduction
PHASER	phasing