2AH7

Crystal structure of nitrophorin 2 aqua complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.68	26.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.526	α = 90
b = 34.526	β = 90
c = 255.76	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	bent Si-mirror	2004-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	18.52	99.1	0.07	20	4.9	18316	18316			34.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.76	99.2		0.38	2	3.8	1792

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1PEE	1.7	18.52	17246	17246	917	99.15	0.1833	0.1833	0.18113	0.22551	RANDOM	23.485

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]
-0.19			-0.19		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.888
r_dihedral_angle_3_deg	13.981
r_dihedral_angle_4_deg	9.184
r_dihedral_angle_1_deg	6.991
r_scangle_it	3.779
r_sphericity_bonded	3.259
r_scbond_it	2.833
r_mcangle_it	1.915
r_angle_refined_deg	1.911
r_mcbond_it	1.644
r_angle_other_deg	1.428
r_mcbond_other	0.35
r_symmetry_vdw_other	0.237
r_nbd_refined	0.184
r_nbd_other	0.18
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.158
r_symmetry_vdw_refined	0.14
r_chiral_restr	0.121
r_nbtor_other	0.088
r_bond_refined_d	0.021
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1432
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
XDISPLAYF	data reduction
d*TREK	data scaling