3GU4 | pdb_00003gu4

Crystal structure of DAPKQ23V-AMPPNP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	0.1 M MES, 1.8 M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.883	α = 90
b = 62.431	β = 90
c = 88.412	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MARMOSAIC 300 mm CCD	Be lenses	2008-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.35	30	98.84	12.7	5.7	57021	57021			20.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.35	1.4	97.33		3.3	5.6	5539

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB entry 1JKS	1.35	29.44	54069	54069	2887	98.84	0.1853	0.18392	0.1834	0.21117	0.2092	RANDOM	17.543

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]
0.06			0.19		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.431
r_dihedral_angle_4_deg	18.87
r_dihedral_angle_3_deg	13.655
r_dihedral_angle_1_deg	5.788
r_scangle_it	2.728
r_scbond_it	1.776
r_angle_refined_deg	1.307
r_mcangle_it	1.276
r_mcbond_it	0.754
r_nbtor_refined	0.309
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.182
r_symmetry_hbond_refined	0.128
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.085
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2470
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	31

Software

Software
Software Name	Purpose
BLU-MAX	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling