2RH6

Structure of Xac NPP for evaluation of refinement methodology

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GSN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	0.1M Bis-Tris HCl, 19% PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.049	α = 90
b = 78.62	β = 90
c = 129.953	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	100	CCD	ADSC QUANTUM 315		2005-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2		ALS	8.2.2

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	1.4	50	87.2	0.136			110794	110794

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2GSN	1.45	39.9	93861	4886	82.24	0.18675	0.18547	0.21063	RANDOM	16.705

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			-0.02		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.207
r_dihedral_angle_3_deg	12.659
r_dihedral_angle_4_deg	11.314
r_dihedral_angle_1_deg	5.881
r_scangle_it	2.334
r_scbond_it	1.583
r_angle_refined_deg	1.294
r_mcangle_it	0.999
r_mcbond_it	0.87
r_angle_other_deg	0.82
r_symmetry_vdw_other	0.278
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.197
r_nbd_other	0.19
r_mcbond_other	0.184
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.135
r_symmetry_hbond_refined	0.116
r_nbtor_other	0.081
r_chiral_restr	0.079
r_metal_ion_refined	0.06
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5882
Nucleic Acid Atoms
Solvent Atoms	669
Heterogen Atoms	73

Software

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