9DUI | pdb_00009dui

Re-refined of Crystal structure of dopa decarboxylase in complex with the inhibitor carbidopa (1JS3) with ketoenamine form of carbidopa

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	PEG MME 5000, MES, ammonium sulfate at pH 6.5, VAPOR DIFFUSION, HANGING DROP at 298K, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.36	α = 90
b = 154.36	β = 90
c = 86.78	γ = 120

Symmetry
Space Group	P 62

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		1993-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LURE BEAMLINE D41A	0.9500	LURE	D41A

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	2.25	19.611	95.8	0.056	9.5	2.9		53582			15

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	2.25	2.3	70.7		0.19	4.7	1.7

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.25	19.61	53582	2540	95.781	0.119	0.1171	0.1294	0.1538	0.1594	RANDOM	23.854

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]
-0.021	-0.01		-0.021		0.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.98
r_dihedral_angle_3_deg	13.882
r_dihedral_angle_2_deg	9.41
r_lrange_it	8.333
r_lrange_other	8.306
r_scangle_it	7.218
r_scangle_other	7.102
r_dihedral_angle_1_deg	6.434
r_scbond_it	5.11
r_scbond_other	5.045
r_mcangle_other	3.042
r_mcangle_it	3.041
r_mcbond_it	2.258
r_mcbond_other	2.256
r_angle_refined_deg	1.697
r_angle_other_deg	0.588
r_nbd_refined	0.222
r_nbtor_refined	0.19
r_symmetry_nbd_refined	0.189
r_symmetry_nbd_other	0.187
r_nbd_other	0.179
r_symmetry_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_refined	0.15
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.084
r_ncsr_local_group_1	0.053
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7284
Nucleic Acid Atoms
Solvent Atoms	579
Heterogen Atoms	82

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	model building
DM	phasing