4WHO | pdb_00004who

Resting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3T63

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	1.2 M Ammonium Sulfate, 2.5 mM 2-mercaptoethanol, 100 mM Tris-HCl pH 8.5; 2:1 ratio of well sol. to 40 mg/ml protein solution in drop

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.092	α = 90
b = 140.636	β = 90
c = 168.66	γ = 90

Symmetry
Space Group	I 2 2 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		2014-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.83	50	90.9	0.162	0.184	0.086	13.1	4.6		121908

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.86	99.9		0.453	0.513	0.236	0.848		4.6	6629

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3T63	1.83	32.45	115055	6094	90.69	0.1819	0.1801	0.1936	0.2158	0.2255	RANDOM	22.134

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]
0.04			-0.05		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.781
r_dihedral_angle_4_deg	16.346
r_dihedral_angle_3_deg	14.153
r_dihedral_angle_1_deg	6.531
r_angle_refined_deg	1.516
r_angle_other_deg	0.824
r_chiral_restr	0.101
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10338
Nucleic Acid Atoms
Solvent Atoms	916
Heterogen Atoms	15

Software

Software
Software Name	Purpose
HKL-3000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
DENZO	data reduction
SCALEPACK	data scaling