3AGC | pdb_00003agc

F218V mutant of the substrate-bound 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	2ZXL	PDB ENTRY 2ZXL

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
1.99	38.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.089	α = 90
b = 84.321	β = 90
c = 131.518	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	RIGAKU JUPITER 210		2009-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.000	SPring-8	BL38B1

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	20	99.6	0.059	10.6	5.9	34491	34491

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	2.07	100		0.356	8	6	3425

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZXL	2	20	32702	32702	1735	99.47	0.21181	0.21181	0.20885	0.23	0.26992	0.28	RANDOM	20.784

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]
-0.08			-0.32		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.591
r_dihedral_angle_4_deg	18.259
r_dihedral_angle_3_deg	16.736
r_dihedral_angle_1_deg	5.457
r_scangle_it	1.965
r_angle_refined_deg	1.526
r_scbond_it	1.166
r_mcangle_it	0.828
r_mcbond_it	0.428
r_nbtor_refined	0.295
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.173
r_symmetry_hbond_refined	0.139
r_xyhbond_nbd_refined	0.112
r_metal_ion_refined	0.088
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
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	4225
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	48

Software

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