5JCK

Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4H4Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	Tris, lithium sulfate, PEG 5000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.473	α = 90
b = 81.473	β = 90
c = 121.357	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 315r		2015-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97954	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	50	99.7	0.145	5.7	14.1		53422

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	100		0.355		14.4	2673

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4H4Q	2	50	26925	1360	99.45	0.1474	0.1444	0.2087	RANDOM	20.488

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]
-0.21			-0.21		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.963
r_dihedral_angle_4_deg	14.685
r_dihedral_angle_3_deg	14.465
r_dihedral_angle_1_deg	6.519
r_mcangle_it	3.055
r_angle_refined_deg	2.225
r_mcbond_it	2.168
r_mcbond_other	2.166
r_angle_other_deg	1.398
r_chiral_restr	0.234

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.963
r_dihedral_angle_4_deg	14.685
r_dihedral_angle_3_deg	14.465
r_dihedral_angle_1_deg	6.519
r_mcangle_it	3.055
r_angle_refined_deg	2.225
r_mcbond_it	2.168
r_mcbond_other	2.166
r_angle_other_deg	1.398
r_chiral_restr	0.234
r_bond_refined_d	0.024
r_gen_planes_refined	0.013
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3278
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	97

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.