2ACP | pdb_00002acp

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	1EUO

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
1.88	34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.754	α = 90
b = 125.642	β = 90
c = 33.468	γ = 90

Symmetry
Space Group	P 21 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	2004-08-04	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	1.4	20	95.4	0.09	25	7.3	32453	32453			29.9

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)
	1.4	1.45	98		0.47	2	6.4	3256

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 (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	FOURIER SYNTHESIS	THROUGHOUT	1EUO	1.4	20	30813	1637	95.42	0.1872	0.1872	0.18479	0.19	0.23279	0.24	RANDOM	25.274

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]
1.06			-0.88		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.648
r_dihedral_angle_3_deg	16.006
r_sphericity_free	9.95
r_dihedral_angle_4_deg	8.535
r_dihedral_angle_1_deg	7.114
r_scangle_it	5.224
r_scbond_it	4.101
r_sphericity_bonded	4.084
r_rigid_bond_restr	3.717
r_mcangle_it	2.895
r_mcbond_it	2.313
r_angle_refined_deg	2.028
r_angle_other_deg	1.451
r_mcbond_other	0.84
r_symmetry_vdw_refined	0.368
r_symmetry_vdw_other	0.311
r_symmetry_hbond_refined	0.238
r_nbd_refined	0.204
r_nbd_other	0.186
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.131
r_nbtor_other	0.092
r_bond_refined_d	0.022
r_gen_planes_refined	0.013
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1442
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	47

Software

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