Experiment: 2F2U

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	0.8M Sodium Citrate, 0.1M Sodium Citrate Buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.76	67.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.531	α = 90
b = 102.531	β = 90
c = 257.185	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	90	CCD	Bruker DIP-6040	a double-crystal monochromator and a horizontal focusing mirror	2003-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	2.4	30	95.8	0.075			53814	52492

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)
	2.4	2.49	81		0.347

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1APM	2.4	30	52481	52481	2663	95.92	0.197	0.197	0.195	0.235	RANDOM	47.404

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	39.593
r_dihedral_angle_4_deg	23.701
r_dihedral_angle_3_deg	15.077
r_scangle_it	6.071
r_scbond_it	3.866
r_mcangle_it	2.547
r_dihedral_angle_1_deg	2.384
r_angle_refined_deg	1.681
r_mcbond_it	1.348
r_nbtor_refined	0.324

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.593
r_dihedral_angle_4_deg	23.701
r_dihedral_angle_3_deg	15.077
r_scangle_it	6.071
r_scbond_it	3.866
r_mcangle_it	2.547
r_dihedral_angle_1_deg	2.384
r_angle_refined_deg	1.681
r_mcbond_it	1.348
r_nbtor_refined	0.324
r_symmetry_vdw_refined	0.262
r_nbd_refined	0.248
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.115
r_symmetry_hbond_refined	0.105
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6211
Nucleic Acid Atoms
Solvent Atoms	162
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.