7COV | pdb_00007cov

Potato D-enzyme, native (substrate free)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		273	12% PEG 8000, 100 mM HEPES (pH 7.6), 100 mM CaCl2

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.869	α = 90
b = 120.535	β = 90
c = 174.381	γ = 90

Symmetry
Space Group	C 2 2 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		2004-11-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	35.36	99.2	0.032	1	44.2	7.3		49562

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11			0.092	0.996

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)	Mean Isotropic B
X-RAY DIFFRACTION	MAD	FREE R-VALUE	2	35.36	49547	2503	98.955	0.152	0.1505	0.1623	0.1878	0.1971	26.523

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]
-0.003			0.005		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.442
r_dihedral_angle_4_deg	18.139
r_dihedral_angle_3_deg	13.773
r_lrange_it	8.412
r_lrange_other	8.243
r_dihedral_angle_1_deg	6.544
r_scangle_it	5.758
r_scangle_other	5.757
r_mcangle_other	4.366
r_mcangle_it	4.365
r_scbond_it	3.76
r_scbond_other	3.759
r_mcbond_it	3.034
r_mcbond_other	3
r_angle_other_deg	2.474
r_angle_refined_deg	1.803
r_symmetry_nbd_other	0.222
r_nbd_other	0.22
r_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.18
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.147
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.079
r_bond_other_d	0.034
r_gen_planes_other	0.017
r_bond_refined_d	0.013
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4183
Nucleic Acid Atoms
Solvent Atoms	605
Heterogen Atoms	49

Software

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