3EJ6 | pdb_00003ej6

Neurospora Crassa Catalase-3 Crystal Structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SY7	PDB ENTRY 1SY7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	291	18% PEG 4000, 50MM TRIS, pH 8.00, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.835	α = 90
b = 154.507	β = 90
c = 162.415	γ = 90

Symmetry
Space Group	P 21 21 21

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		2002-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.97950	NSLS	X6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.3	34.68	93.5	0.083	0.087	7.2	3.7		152747			20.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	85.8		0.36	0.333	1.7	3

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 1SY7	2.3	34.67	136823		92.8	0.237	0.193	0.24	0.242	0.23	RANDOM	18.52

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]
-0.47			1.17		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.114
r_dihedral_angle_4_deg	11.89
r_dihedral_angle_3_deg	11.499
r_dihedral_angle_1_deg	4.611
r_angle_refined_deg	0.763
r_angle_other_deg	0.752
r_nbtor_refined	0.165
r_nbd_other	0.161
r_nbd_refined	0.145
r_scangle_it	0.11
r_symmetry_vdw_refined	0.1
r_symmetry_vdw_other	0.097
r_metal_ion_refined	0.089
r_nbtor_other	0.082
r_scbond_it	0.079
r_xyhbond_nbd_refined	0.075
r_symmetry_hbond_refined	0.057
r_chiral_restr	0.043
r_mcbond_it	0.036
r_mcangle_it	0.034
r_bond_other_d	0.007
r_bond_refined_d	0.005
r_mcbond_other	0.004
r_gen_planes_refined	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21360
Nucleic Acid Atoms
Solvent Atoms	1365
Heterogen Atoms	284

Software

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