1YDG | pdb_00001ydg

Crystal Structure of Trp repressor binding protein WrbA

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	4.5	293	2.6M AmSulfate, 20% Glycerol, pH 4.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.611	α = 90
b = 121.611	β = 90
c = 207.933	γ = 120

Symmetry
Space Group	P 32 2 1

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	MARRESEARCH		2003-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	.9793	APS	31-ID

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	20	97	0.086	13	3.6	120346	116736		-3

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)
	2	2.07	99.8		0.29	5.6		11858

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	2	20	-3	116506	116506	5845	96.86	0.18877	0.18877	0.18632	0.2	0.23551	0.24	RANDOM	22.254

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]
0.25	0.12		0.25		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.61
r_dihedral_angle_4_deg	15.58
r_dihedral_angle_3_deg	13.83
r_dihedral_angle_1_deg	5.869
r_scangle_it	2.376
r_scbond_it	1.546
r_angle_refined_deg	1.182
r_mcangle_it	1.155
r_mcbond_it	1.053
r_angle_other_deg	0.767
r_symmetry_vdw_refined	0.273
r_symmetry_vdw_other	0.212
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.194
r_nbd_other	0.181
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.168
r_mcbond_other	0.128
r_xyhbond_nbd_other	0.087
r_nbtor_other	0.084
r_chiral_restr	0.062
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12056
Nucleic Acid Atoms
Solvent Atoms	1293
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing