3AGB | pdb_00003agb

F218V mutant of the substrate-free form of red chlorophyll catabolite reductase from Arabidopsis thaliana

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AGA	PDB ENTRY 3AGA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	35% PEG 2000 monomethyl ether, 0.1M ammonium acetate, 3% dioxane, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.141	α = 90
b = 84.431	β = 90
c = 132.248	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	RAYONIX MX225HE		2009-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	50	98.9	0.077	11.6	8.2	26102	26102

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	96.8		0.359	6.9	6.9	2523

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3AGA	2.2	35.58	24795	24795	1330	98.53	0.22448	0.22448	0.22087	0.24	0.29191	0.31	RANDOM	22.84

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]
-0.45			-0.89		1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.857
r_dihedral_angle_4_deg	19.333
r_dihedral_angle_3_deg	18.25
r_dihedral_angle_1_deg	5.799
r_scangle_it	2.399
r_scbond_it	1.453
r_angle_refined_deg	1.266
r_mcangle_it	0.975
r_mcbond_it	0.508
r_nbtor_refined	0.299
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.085
r_metal_ion_refined	0.062
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4195
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	2

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling