3DGN | pdb_00003dgn

A non-biological ATP binding protein crystallized in the presence of 100 mM ADP

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	sitting drop vapor diffusion	8.5	298	0.1 M sodium phosphate, 0.25 M sodium citrate, 0.3 M sodium chloride, 23% polyethylene glycol 400, 0.2 M ammonium acetate, pH 8.5, sitting drop vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.38	71.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.383	α = 90
b = 72.383	β = 90
c = 54.777	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	143	IMAGE PLATE	RIGAKU RAXIS IV++	mirrors	2008-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE		1.5418

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	2.7	25	99.1	0.283	5	6.5		4736

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.8	99.8			6.5	469

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 (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	2.7	23.7	4720	215	99.01	0.2	0.197	0.2053	0.255	0.2598	RANDOM	27.778

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]
0.1	0.05		0.1		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.095
r_dihedral_angle_3_deg	18.193
r_dihedral_angle_4_deg	9.264
r_dihedral_angle_1_deg	8.504
r_scangle_it	6.113
r_scbond_it	3.704
r_angle_refined_deg	2.955
r_mcangle_it	2.169
r_mcbond_it	1.148
r_chiral_restr	0.196
r_bond_refined_d	0.033
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	587
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	42

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling