3DZR | pdb_00003dzr

Thaumatin by Classical hanging drop method before high X-Ray dose on ESRF ID29 beamline

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RQW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	100mM ADA, 1M Na/K-tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.814	α = 90
b = 57.814	β = 90
c = 150.196	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 315	toroidal mirror	2007-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9787	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.51	53.955	100	0.077	0.077		7.6		41007

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.51	1.59	100		0.105	0.105	6.2	7.8	5857

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	1RQW	1.51	45.83	40938	2056	99.92	0.138	0.137	0.14	0.153	0.15	RANDOM	16.559

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.991
r_dihedral_angle_4_deg	13.343
r_dihedral_angle_3_deg	10.816
r_dihedral_angle_1_deg	6.132
r_scangle_it	2.493
r_mcangle_it	2.329
r_scbond_it	1.518
r_mcbond_it	1.412
r_angle_refined_deg	1.105
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.991
r_dihedral_angle_4_deg	13.343
r_dihedral_angle_3_deg	10.816
r_dihedral_angle_1_deg	6.132
r_scangle_it	2.493
r_mcangle_it	2.329
r_scbond_it	1.518
r_mcbond_it	1.412
r_angle_refined_deg	1.105
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.204
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.076
r_bond_refined_d	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1604
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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 R01GM157729.